EP4018821A1 - Procédés d'identification et de sélection de plants de maïs comportant un gène restaurateur de la stérilité mâle cytoplasmique - Google Patents

Procédés d'identification et de sélection de plants de maïs comportant un gène restaurateur de la stérilité mâle cytoplasmique Download PDF

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Publication number
EP4018821A1
EP4018821A1 EP20216347.3A EP20216347A EP4018821A1 EP 4018821 A1 EP4018821 A1 EP 4018821A1 EP 20216347 A EP20216347 A EP 20216347A EP 4018821 A1 EP4018821 A1 EP 4018821A1
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Prior art keywords
plant
maize
identifying
seq
restorer
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EP20216347.3A
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German (de)
English (en)
Inventor
Monika KLOIBER-MAITZ
Carsten Knaak
Hervé DALL'OCCHIO
Jean-Claude CASTELLE
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KWS SAAT SE and Co KGaA
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KWS SAAT SE and Co KGaA
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Application filed by KWS SAAT SE and Co KGaA filed Critical KWS SAAT SE and Co KGaA
Priority to EP20216347.3A priority Critical patent/EP4018821A1/fr
Priority to CA3202093A priority patent/CA3202093A1/fr
Priority to PCT/EP2021/087187 priority patent/WO2022136491A1/fr
Priority to ARP210103628A priority patent/AR124476A1/es
Priority to CN202180094251.9A priority patent/CN116887669A/zh
Priority to EP21823713.9A priority patent/EP4266873A1/fr
Priority to US18/268,901 priority patent/US20240057538A1/en
Publication of EP4018821A1 publication Critical patent/EP4018821A1/fr
Priority to CL2023001795A priority patent/CL2023001795A1/es
Withdrawn legal-status Critical Current

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    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01H—NEW PLANTS OR NON-TRANSGENIC PROCESSES FOR OBTAINING THEM; PLANT REPRODUCTION BY TISSUE CULTURE TECHNIQUES
    • A01H1/00—Processes for modifying genotypes ; Plants characterised by associated natural traits
    • A01H1/04—Processes of selection involving genotypic or phenotypic markers; Methods of using phenotypic markers for selection
    • A01H1/045—Processes of selection involving genotypic or phenotypic markers; Methods of using phenotypic markers for selection using molecular markers
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01H—NEW PLANTS OR NON-TRANSGENIC PROCESSES FOR OBTAINING THEM; PLANT REPRODUCTION BY TISSUE CULTURE TECHNIQUES
    • A01H6/00—Angiosperms, i.e. flowering plants, characterised by their botanic taxonomy
    • A01H6/46—Gramineae or Poaceae, e.g. ryegrass, rice, wheat or maize
    • A01H6/4684—Zea mays [maize]
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01H—NEW PLANTS OR NON-TRANSGENIC PROCESSES FOR OBTAINING THEM; PLANT REPRODUCTION BY TISSUE CULTURE TECHNIQUES
    • A01H1/00—Processes for modifying genotypes ; Plants characterised by associated natural traits
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01H—NEW PLANTS OR NON-TRANSGENIC PROCESSES FOR OBTAINING THEM; PLANT REPRODUCTION BY TISSUE CULTURE TECHNIQUES
    • A01H1/00—Processes for modifying genotypes ; Plants characterised by associated natural traits
    • A01H1/02—Methods or apparatus for hybridisation; Artificial pollination ; Fertility
    • A01H1/022—Genic fertility modification, e.g. apomixis
    • A01H1/023—Male sterility
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01H—NEW PLANTS OR NON-TRANSGENIC PROCESSES FOR OBTAINING THEM; PLANT REPRODUCTION BY TISSUE CULTURE TECHNIQUES
    • A01H5/00—Angiosperms, i.e. flowering plants, characterised by their plant parts; Angiosperms characterised otherwise than by their botanic taxonomy
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
    • C12N15/8261—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield
    • C12N15/8287—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for fertility modification, e.g. apomixis
    • C12N15/8289—Male sterility
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • C12Q1/6895—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for plants, fungi or algae
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/13—Plant traits
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/172—Haplotypes

Definitions

  • the invention relates to methods for identifying plants or plant parts, in particular maize plants or plant parts having a restorer of fertility genotype or phenotype, in particular a cytoplasmic fertility restorer of fertility genotype or phenotype.
  • the present invention also relates to plants identified as such, as well as methods for generating such plants.
  • the present invention further relates to polynucleic acids and polypeptides suitable for identifying or generating such plants.
  • CMS cytoplasmic male sterility
  • the major restorer locus RF4 at the beginning of chromosome 8 is well known ( WO 2012/047595 ). Before conversion of a female line to CMSC, it has to be guaranteed, that RF4 is not active in this line. Otherwise, the maintainer locus has to be introgressed before CMS conversion is possible. Defining restorer genotype is done both by marker application and by phenotypic observations.
  • the identification of new restorer genotypes, in particular different from the restorer genotypes already known on maize chromosome 8 expands their usability in plant breeding, in particular introgression.
  • the present invention relates to plants or plant parts, in particular maize plants or plants parts having a restorer genotype or phenotype and their use.
  • the restorer genotype or phenotype in particular refers to a cytoplasmic male sterility (CMS) restorer genotype or phenotype, i.e. a genotype or phenotype which restores male fertility.
  • CMS cytoplasmic male sterility
  • the restorer genotype is caused by one or more restorer genes which are located on maize chromosome 3, i.e. RF-03-01.
  • the present invention advantageously allows to identify maize lines having a CMS restorer phenotype, which comprise well known restorer genes or loci, such as RF4.
  • the different chromosomal location of the restorer locus of the present invention compared to known restorer loci expands the tool kit for generating as well as maintaining restorer lines, or alternatively for ensuring that an unwanted restorer genotype/phenotype remains absent or can be selected against.
  • a method for identifying a (maize) plant or plant part comprising screening for the presence of, detecting, or identifying (a haplotype associated with) a cytoplasmic male sterility (CMS) (fertility) restorer locus on chromosome 3 (RF-03-01).
  • CMS cytoplasmic male sterility
  • RF-03-01 cytoplasmic male sterility
  • locus comprises or is comprised in a region on chromosome 3 corresponding to positions 197453646 to 197698278 of B73 AGPv4, or a fragment thereof. 4.
  • locus comprises one or more of molecular marker(s) (alleles) of Table 4 or Table 5 .
  • locus comprises one or more of a polynucleic acid comprising one or more of SEQ ID NOs: 17 to 200 .
  • said locus comprises one or more of a polynucleic acid comprising one or more of SEQ ID NOs: 68 to 140. 7.
  • the terms "one or more” or “at least one”, such as one or more or at least one member(s) of a group of members, is clear per se, by means of further exemplification, the term encompasses inter alia a reference to any one of said members, or to any two or more of said members, such as, e.g., any ⁇ 3, ⁇ 4, ⁇ 5, ⁇ 6 or ⁇ 7 etc. of said members, and up to all said members.
  • plant includes whole plants, including descendants or progeny thereof. As used herein unless clearly indicated otherwise, the term “plant” intends to mean a plant at any developmental stage.
  • plant part includes any part or derivative of the plant, including particular plant tissues or structures, plant cells, plant protoplast, plant cell or tissue culture from which plants can be regenerated, plant calli, plant clumps and plant cells that are intact in plants or parts of plants, such as seeds, kernels, cobs, flowers, cotyledons, leaves, stems, buds, roots, root tips, stover, and the like. Plant parts may include processed plant parts or derivatives, including flower, oils, extracts etc. "Parts of a plant” are e.g.
  • shoot vegetative organs/structures e.g., leaves, stems and tubers; roots, flowers and floral organs/structures, e.g. bracts, sepals, petals, stamens, carpels, anthers and ovules; seed, including embryo, endosperm, and seed coat; fruit and the mature ovary; plant tissue, e.g. vascular tissue, ground tissue, and the like; and cells, e.g. guard cells, egg cells, pollen, trichomes and the like; and progeny of the same.
  • Parts of plants may be attached to or separate from a whole intact plant. Such parts of a plant include, but are not limited to, organs, tissues, and cells of a plant, and preferably seeds.
  • a “plant cell” is a structural and physiological unit of a plant, comprising a protoplast and a cell wall.
  • the plant cell may be in form of an isolated single cell or a cultured cell, or as a part of higher organized unit such as, for example, plant tissue, a plant organ, or a whole plant.
  • Plant cell culture means cultures of plant units such as, for example, protoplasts, cell culture cells, cells in plant tissues, pollen, pollen tubes, ovules, embryo sacs, zygotes and embryos at various stages of development.
  • Plant material refers to leaves, stems, roots, flowers or flower parts, fruits, pollen, egg cells, zygotes, seeds, cuttings, cell or tissue cultures, or any other part or product of a plant, including meal. This also includes callus or callus tissue as well as extracts (such as extracts from taproots) or samples.
  • a "plant organ” is a distinct and visibly structured and differentiated part of a plant such as a root, stem, leaf, flower bud, or embryo.
  • Plant tissue as used herein means a group of plant cells organized into a structural and functional unit. Any tissue of a plant in planta or in culture is included.
  • This term includes, but is not limited to, whole plants, plant organs, plant seeds, tissue culture and any groups of plant cells organized into structural and/or functional units.
  • the use of this term in conjunction with, or in the absence of, any specific type of plant tissue as listed above or otherwise embraced by this definition is not intended to be exclusive of any other type of plant tissue.
  • the plant part or derivative is or comprises (functional) propagation material, such as germplasm, a seed, or plant embryo or other material from which a plant can be regenerated. In certain embodiments, the plant part or derivative is not (functional) propagation material, such as germplasm, a seed, or plant embryo or other material from which a plant can be regenerated. In certain embodiments, the plant part or derivative does not comprise (functional) male and female reproductive organs.
  • the plant part or derivative is or comprises propagation material, but propagation material which does not or cannot be used (anymore) to produce or generate new plants, such as propagation material which have been chemically, mechanically or otherwise rendered non-functional, for instance by heat treatment, acid treatment, compaction, crushing, chopping, etc.
  • progeny and “progeny plant” refer to a plant generated from sexual reproduction from one or more parent plants.
  • a progeny plant can be obtained by selfing a single parent plant, or by crossing two parental plants.
  • a progeny plant can be obtained by selfing of a parent plant or by crossing two parental plants and include selfings as well as the F1 or F2 or still further generations.
  • An F1 is a first-generation progeny produced from parents at least one of which is used for the first time as donor of a trait, while progeny of second generation (F2) or subsequent generations (F3 , F4 , and the like) are specimens produced from selfings, intercrosses, backcrosses, and/or other crosses of F1 s, F2 s, and the like.
  • An F1 can thus be (and in some embodiments is) a hybrid resulting from a cross between two true breeding parents (i.e., parents that are true-breeding are each homozygous for a trait of interest or an allele thereof), while an F2 can be (and in some embodiments is) a progeny resulting from self-pollination of the F1 hybrids.
  • the term "progeny” can in certain embodiments be used interchangeably with "offspring", in particular when the plant or plant material is derived from sexual crossing of parent plants. According to the present invention, progeny preferably refers to the F1 progeny.
  • crossing means the fusion of gametes via pollination to produce progeny (i.e., cells, seeds, or plants).
  • the term encompasses both sexual crosses (the pollination of one plant by another) and self-fertilization (selfing, self-pollination, i.e., when the pollen and ovule (or microspores and megaspores) are from the same plant or genetically identical plants).
  • crossing as referred to herein fertilization of one plant by another plant, i.e. not self-pollination.
  • plant population may be used interchangeably with population of plants.
  • a plant population preferably comprises a multitude of individual plants, such as preferably at least 10, such as 20, 30, 40, 50, 60, 70, 80, or 90, more preferably at least 100, such as 200, 300, 400, 500, 600, 700, 800, or 900, even more preferably at least 1000, such as at least 10000 or at least 100000.
  • phenotype refers to one or more traits of a plant or plant cell.
  • the phenotype can be observable to the naked eye, or by any other means of evaluation known in the art, e.g., microscopy, biochemical analysis, or an electromechanical assay.
  • a phenotype is directly controlled by a single gene or genetic locus (i.e., corresponds to a "single gene trait”).
  • haploid induction use of color markers, such as R Navajo, and other markers including transgenes visualized by the presences or absences of color within the seed evidence if the seed is an induced haploid seed.
  • R Navajo as a color marker and the use of transgenes is well known in the art as means to detect induction of haploid seed on the female plant.
  • a phenotype is the result of interactions among several genes, which in some embodiments also results from an interaction of the plant and/or plant cell with its environment.
  • maize refers to a plant of the species Zea mays, preferably Zea mays ssp mays.
  • male sterile plant line, cultivar, or variety
  • the term refers to a plant which is unable to produce offspring as a pollen donor, and may result from the failure to produce (functional) anthers, pollen, or gametes.
  • Cytoplasmic male sterile plants have cytoplasmic genes, usually in the mitochondria, that encode factors that disrupt or prevent pollen development, making them male-sterile, with male sterility inherited maternally.
  • cytoplasmic male sterility for hybrid seed production typically requires three separate plant lines: the male-sterile line, an isogeneic male-fertile line for propagation ("maintainer line”) and a line for restoring fertility to the hybrid so that it can produce seed (“restorer line”).
  • the male-sterile line is used as the receptive parent in a hybrid cross
  • the maintainer line is genetically identical to the male-sterile line, excepting that it lacks the cytoplasmic sterility factors
  • the restorer line is any line that masks the cytoplasmic sterility factor.
  • the restorer line is very important for those plants, such as grain sorghum or cotton, the useful crop of which is the seed itself or seed-associated structures.
  • genetic male sterility is similar to cytoplasmic male sterility, but differs in that the sterility factors are encoded in nuclear DNA. Typically, genetic male sterility refers to a change in a plant's genetic structure which results in its ability to produce and/or spread viable pollen. Genetic male sterile plant lines may occur naturally. It is also possible to create a male-sterile plant line using recombinant techniques. Whether naturally occurring or transgenic, male-sterile lines still require the use of a sister maintainer line for their propagation, which of necessity leads to a minimum of 50% male-fertile plants in propagated seed. This is a result of the genetics of male-sterility and maintainer lines.
  • male sterility refers to genetical male sterility.
  • male sterility is not or does not encompass cytoplasmic male sterility.
  • CMS as referred to herein is CMS-C (or C-type CMS), although other types of CMS are also envisaged, including CMS-T and CMS-S.
  • the term “restorer” or “restorer of fertility” means the gene(s) that restore(s) fertility to a CMS plant.
  • the term “restorer” may also mean the plant or line carrying the restorer gene.
  • the term restorer can be applied to a restorer locus (allele), haplotype, or genotype, meaning a locus (allele), haplotype, or genotype carrying the restores gene or being responsible for the restorer phenotype.
  • the restorer gene, locus (allele), haplotype, genotype, or phenotype is associated/linked with the polymorphisms (alleles), polynucleic acids, or markers of the invention as described herein elsewhere.
  • a restorer locus (allele) or fertility restorer locus (allele) refers to a genomic interval carrying the restorer gene(s), and is characterized by the presence of one or more of the polymorphisms (alleles), polynucleic acids, or molecular markers as described herein.
  • the restorer is not (solely) or does not (solely) comprise Rf4.
  • marker(s) allele(s) of the invention
  • a marker haplotype of the invention The combination of any one or more of the marker(s) (allele(s)) of the invention may be referred to as a marker haplotype of the invention.
  • the term "maintainer” may equally be used for the male fertile as well as the (isogenic) male sterile lines, and hence refers to a plant (or line) which does not have the restorer phenotype and/or comprise the restorer genotype, haplotype, or locus (allele) (all either heterozygous or homozygous), as opposed to the term “restorer”, which does have the restorer phenotype and/or comprises the restorer genotype, haplotype, or (allele) (all either heterozygous or homozygous), preferably the restorer phenotype, genotype, haplotype or locus (allele) of the present invention.
  • the term “maintainer” may be used equally for the maintainer line sensu strictu, i.e. the isogenic fertile counterpart of the CMS line for use in "maintaining" the CMS line, as well as for the CMS line itself.
  • the maintainer does not have the restorer phenotype and/or comprise the restorer genotype, haplotype, or locus (allele) of the invention, such as any one or more molecular markers (alleles) of the invention, in particular the molecular markers (alleles) associated /linked with the restorer phenotype, genotype, haplotype, or locus (allele) of the invention, which may be homozygous or heterozygous.
  • the maintainer has a different restorer phenotype and/or comprise the restorer genotype, haplotype, or locus (allele) than the restorer phenotype and/or comprise the restorer genotype, haplotype, or locus (allele) of the invention, e.g. Rf4, which may be homozygous or heterozygous.
  • locus means a specific place or places or a site on a chromosome where for example a QTL/haplotype, a gene or genetic marker is found.
  • QTL quantitative trait locus
  • a QTL may refer to a region of DNA that is associated with the differential expression of a quantitative phenotypic trait in at least one genetic background, e.g., in at least one breeding population. The region of the QTL encompasses or is closely linked to the gene or genes that affect the trait in question.
  • allele or “alleles” refers to one or more alternative forms, i.e. different nucleotide sequences, of a locus.
  • An "allele of a locus” can comprise multiple genes or other genetic factors within a contiguous genomic region or linkage group, such as a haplotype.
  • An allele of a locus can denote a haplotype within a specified window wherein said window is a contiguous genomic region that can be defined, and tracked, with a set of one or more polymorphic markers.
  • a haplotype can be defined by the unique fingerprint of alleles at each marker within the specified window.
  • a locus may encode for one or more alleles that affect the expressivity of a continuously distributed (quantitative) phenotype.
  • the locus, allele, polynucleic acid, or molecular marker (allele) as described herein may be homozygous.
  • the locus, allele, polynucleic acid, or molecular marker (allele) as described herein may be heterozygous.
  • mutant alleles or “mutation” of alleles include alleles having one or more mutations, such as insertions, deletions, stop codons, base changes (e.g. , transitions or transversions), or alterations in splice junctions, which may or may not give rise to altered gene products. Modifications in alleles may arise in coding or non-coding regions (e.g. promoter regions, exons, introns or splice junctions).
  • a “marker” is a (means of finding a position on a) genetic or physical map, or else linkages among markers and trait loci (loci affecting traits).
  • the position that the marker detects may be known via detection of polymorphic alleles and their genetic mapping, or else by hybridization, sequence match or amplification of a sequence that has been physically mapped.
  • a marker can be a DNA marker (detects DNA polymorphisms), a protein (detects variation at an encoded polypeptide), or a simply inherited phenotype (such as the 'waxy' phenotype).
  • a DNA marker can be developed from genomic nucleotide sequence or from expressed nucleotide sequences (e.g., from a spliced RNA or a cDNA). Depending on the DNA marker technology, the marker may consist of complementary primers flanking the locus and/or complementary probes that hybridize to polymorphic alleles at the locus.
  • the term marker locus is the locus (gene, sequence or nucleotide) that the marker detects.
  • Marker or “molecular marker” or “marker locus” may also be used to denote a nucleic acid or amino acid sequence that is sufficiently unique to characterize a specific locus on the genome. Any detectable polymorphic trait can be used as a marker so long as it is inherited differentially and exhibits linkage disequilibrium with a phenotypic trait of interest.
  • Markers that detect genetic polymorphisms between members of a population are well-established in the art. Markers can be defined by the type of polymorphism that they detect and also the marker technology used to detect the polymorphism. Marker types include but are not limited to, e.g., detection of restriction fragment length polymorphisms (RFLP), detection of isozyme markers, randomly amplified polymorphic DNA (RAPD), amplified fragment length polymorphisms (AFLPs), detection of simple sequence repeats (SSRs), detection of amplified variable sequences of the plant genome, detection of self-sustained sequence replication, or detection of single nucleotide polymorphisms (SNPs). SNPs can be detected e.g.
  • RFLP restriction fragment length polymorphisms
  • RAPD randomly amplified polymorphic DNA
  • AFLPs amplified fragment length polymorphisms
  • SSRs simple sequence repeats
  • SNPs single nucleotide polymorphisms
  • DNA sequencing via DNA sequencing, PCR-based sequence specific amplification methods, detection of polynucleotide polymorphisms by allele specific hybridization (ASH), dynamic allele-specific hybridization (DASH), molecular beacons, microarray hybridization, oligonucleotide ligase assays, Flap endonucleases, 5' endonucleases, primer extension, single strand conformation polymorphism (SSCP) or temperature gradient gel electrophoresis (TGGE).
  • DNA sequencing such as the pyrosequencing technology has the advantage of being able to detect a series of linked SNP alleles that constitute a haplotype. Haplotypes tend to be more informative (detect a higher level of polymorphism) than SNPs.
  • a “marker allele”, alternatively an “allele of a marker locus”, can refer to one of a plurality of polymorphic nucleotide sequences found at a marker locus in a population.
  • allele refers to the specific nucleotide base present at that SNP locus in that individual plant.
  • “Fine-mapping” refers to methods by which the position of a genomic region (e.g. QTL) can be determined more accurately (narrowed down) and by which the size of the introgression fragment comprising the QTL is reduced.
  • a genomic region e.g. QTL
  • haplotype-NILs Near Isogenic Lines for the QTL or haplotype
  • Such lines can then be used to map on which fragment the QTL/haplotype is located and to identify a line having a shorter introgression fragment comprising the QTL/haplotype.
  • Marker assisted selection (of MAS) is a process by which individual plants are selected based on marker genotypes.
  • Marker assisted counter-selection is a process by which marker genotypes are used to identify plants that will not be selected, allowing them to be removed from a breeding program or planting.
  • Marker assisted selection uses the presence of molecular markers, which are genetically linked to a particular locus or to a particular chromosome region (e.g. introgression fragment, transgene, polymorphism, mutation, etc), to select plants for the presence of the specific locus or region (introgression fragment, transgene, polymorphism, mutation, etc).
  • a molecular marker genetically linked to a genomic region e.g.
  • haplotype or gene (e.g. the RLK1 allele conferring pathogen resistance) as defined herein, can be used to detect and/or select plants comprising the HT2/HT3 on chromosome 8.
  • the closer the genetic linkage of the molecular marker to the locus e.g. about 7 cM, 6 cM, 5 cM, 4 cM, 3 cM, 2 cM, 1 cM, 0.5 cM or less), the less likely it is that the marker is dissociated from the locus through meiotic recombination.
  • the closer two markers are linked to each other e.g.
  • a marker "within 7 cM or within 5 cM, 3 cM, 2 cM, or 1 cM" of another marker refers to a marker which genetically maps to within the 7 cM or 5 cM, 3 cM, 2 cM, or 1 cM region flanking the marker (i.e. either side of the marker).
  • a marker within 5 Mb, 3 Mb, 2.5 Mb, 2 Mb, 1 Mb, 0.5 Mb, 0.4 Mb, 0.3 Mb, 0.2 Mb, 0.1 Mb, 50 kb, 20 kb, 10kb, 5kb, 2kb, 1 kb or less of another marker refers to a marker which is physically located within the 5 Mb, 3 Mb, 2.5 Mb, 2 Mb, 1 Mb, 0.5 Mb, 0.4 Mb, 0.3 Mb, 0.2 Mb, 0.1 Mb, 50 kb, 20 kb, 10 kb, 5 kb, 2 kb, 1 kb or less, of the genomic DNA region flanking the marker (i.e. either side of the marker).
  • LOD-score logarithm (base 10) of odds refers to a statistical test often used for linkage analysis in animal and plant populations. The LOD score compares the likelihood of obtaining the test data if the two loci (molecular marker loci and/or a phenotypic trait locus) are indeed linked, to the likelihood of observing the same data purely by chance. Positive LOD scores favour the presence of linkage and a LOD score greater than 3.0 is considered evidence for linkage. A LOD score of +3 indicates 1000 to 1 odds that the linkage being observed did not occur by chance.
  • a “marker haplotype” refers to a combination of (marker) alleles at a (marker) locus.
  • a "marker locus” is a specific chromosome location in the genome of a species where a specific marker can be found.
  • a marker locus can be used to track the presence of a second linked locus, e.g., one that affects the expression of a phenotypic trait.
  • a marker locus can be used to monitor segregation of alleles at a genetically or physically linked locus.
  • a “marker probe” is a nucleic acid sequence or molecule that can be used to identify the presence of a marker locus, e.g., a nucleic acid probe that is complementary to a marker locus sequence, through nucleic acid hybridization. Marker probes comprising 30 or more contiguous nucleotides of the marker locus ("all or a portion" of the marker locus sequence) may be used for nucleic acid hybridization. Alternatively, in some aspects, a marker probe refers to a probe of any type that is able to distinguish (i.e., genotype) the particular allele that is present at a marker locus.
  • molecular marker may be used to refer to a genetic marker or an encoded product thereof (e.g., a protein) used as a point of reference when identifying a linked locus.
  • a marker can be derived from genomic nucleotide sequences or from expressed nucleotide sequences (e.g., from a spliced RNA, a cDNA, etc.), or from an encoded polypeptide.
  • the term also refers to nucleic acid sequences complementary to or flanking the marker sequences, such as nucleic acids used as probes or primer pairs capable of amplifying the marker sequence.
  • a “molecular marker probe” is a nucleic acid sequence or molecule that can be used to identify the presence of a marker locus, e.g., a nucleic acid probe that is complementary to a marker locus sequence.
  • a marker probe refers to a probe of any type that is able to distinguish (i.e., genotype) the particular allele that is present at a marker locus.
  • Nucleic acids are "complementary" when they specifically hybridize in solution, e.g., according to Watson-Crick base pairing rules. Some of the markers described herein are also referred to as hybridization markers when located on an indel region, such as the non- collinear region described herein.
  • the insertion region is, by definition, a polymorphism vis a vis a plant without the insertion.
  • the marker need only indicate whether the indel region is present or absent. Any suitable marker detection technology may be used to identify such a hybridization marker, e.g. SNP technology is used in the examples provided herein.
  • Genetic markers are nucleic acids that are polymorphic in a population and where the alleles of which can be detected and distinguished by one or more analytic methods, e.g., RFLP, AFLP, isozyme, SNP, SSR, and the like.
  • the terms "molecular marker” and “genetic marker” are used interchangeably herein.
  • the term also refers to nucleic acid sequences complementary to the genomic sequences, such as nucleic acids used as probes. Markers corresponding to genetic polymorphisms between members of a population can be detected by methods well- established in the art.
  • PCR-based sequence specific amplification methods include, e.g., PCR-based sequence specific amplification methods, detection of restriction fragment length polymorphisms (RFLP), detection of isozyme markers, detection of polynucleotide polymorphisms by allele specific hybridization (ASH), detection of amplified variable sequences of the plant genome, detection of self-sustained sequence replication, detection of simple sequence repeats (SSRs), detection of single nucleotide polymorphisms (SNPs), or detection of amplified fragment length polymorphisms (AFLPs).
  • ESTs expressed sequence tags
  • SSR markers derived from EST sequences and randomly amplified polymorphic DNA (RAPD).
  • a polynucleic acid of the invention as described herein is said to be flanked by certain molecular markers or molecular marker alleles if the polynucleic acid is comprised within a polynucleic acid wherein respectively a first marker (allele) is located upstream (i.e. 5') of said polynucleic acid and a second marker (allele) is located downstream (i.e. 3') of said polynucleic acid.
  • first and second marker (allele) may border the polynucleic acid.
  • the nucleic acid may equally comprise such first and second marker (allele), such as respectively at or near the 5' and 3' end, for instance respectively within 50 kb of the 5' and 3' end, preferably within 10 kb of the 5' and 3' end, such as within 5 kb of the 5' and 3' end, within 1 kb of the 5' and 3' end, or less.
  • first and second marker allele
  • a "polymorphism” is a variation in the DNA between two or more individuals within a population.
  • a polymorphism preferably has a frequency of at least 1 % in a population.
  • a useful polymorphism can include a single nucleotide polymorphism (SNP), a simple sequence repeat (SSR), or an insertion/deletion polymorphism, also referred to herein as an "indel".
  • SNP single nucleotide polymorphism
  • SSR simple sequence repeat
  • an insertion/deletion polymorphism also referred to herein as an "indel”.
  • the term “indel” refers to an insertion or deletion, wherein one line may be referred to as having an inserted nucleotide or piece of DNA relative to a second line, or the second line may be referred to as having a deleted nucleotide or piece of DNA relative to the first line.
  • “Physical distance” between loci (e.g. between molecular markers and/or between phenotypic markers) on the same chromosome is the actually physical distance expressed in bases or base pairs (bp), kilo bases or kilo base pairs (kb) or megabases or mega base pairs (Mb).
  • Genetic distance between loci is measured by frequency of crossing-over, or recombination frequency (RF) and is indicated in centimorgans (cM).
  • RF recombination frequency
  • cM centimorgans
  • One cM corresponds to a recombination frequency of 1%. If no recombinants can be found, the RF is zero and the loci are either extremely close together physically or they are identical. The further apart two loci are, the higher the RF.
  • a "physical map" of the genome is a map showing the linear order of identifiable landmarks (including genes, markers, etc.) on chromosome DNA.
  • the distances between landmarks are absolute (for example, measured in base pairs or isolated and overlapping contiguous genetic fragments) and not based on genetic recombination (that can vary in different populations).
  • An allele "negatively” correlates with a trait when it is linked to it and when presence of the allele is an indicator that a desired trait or trait form will not occur in a plant comprising the allele.
  • An allele "positively” correlates with a trait when it is linked to it and when presence of the allele is an indicator that the desired trait or trait form will occur in a plant comprising the allele.
  • centimorgan is a unit of measure of recombination frequency.
  • One cM is equal to a 1 % chance that a marker at one genetic locus will be separated from a marker at a second locus due to crossing over in a single generation.
  • chromosomal interval designates a contiguous linear span of genomic DNA that resides in planta on a single chromosome.
  • the genetic elements or genes located on a single chromosomal interval are physically linked.
  • the size of a chromosomal interval is not particularly limited.
  • the genetic elements located within a single chromosomal interval are genetically linked, typically with a genetic recombination distance of, for example, less than or equal to 20 cM, or alternatively, less than or equal to 10 cM. That is, two genetic elements within a single chromosomal interval undergo recombination at a frequency of less than or equal to 20% or 10%.
  • closely linked in the present application, means that recombination between two linked loci occurs with a frequency of equal to or less than about 10% (i.e., are separated on a genetic map by not more than 10 cM). Put another way, the closely linked loci co-segregate at least 90% of the time. Marker loci are especially useful with respect to the subject matter of the current disclosure when they demonstrate a significant probability of co-segregation (linkage) with a desired trait (e.g., resistance to gray leaf spot).
  • Closely linked loci such as a marker locus and a second locus can display an inter-locus recombination frequency of 10% or less, preferably about 9% or less, still more preferably about 8% or less, yet more preferably about 7% or less, still more preferably about 6% or less, yet more preferably about 5% or less, still more preferably about 4% or less, yet more preferably about 3% or less, and still more preferably about 2% or less.
  • the relevant loci display a recombination a frequency of about 1 % or less, e.g., about 0.75% or less, more preferably about 0.5% or less, or yet more preferably about 0.25% or less.
  • Two loci that are localized to the same chromosome, and at such a distance that recombination between the two loci occurs at a frequency of less than 10% (e.g., about 9 %, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1 %, 0.75%, 0.5%, 0.25%, or less) are also said to be "proximal to" each other.
  • two different markers can have the same genetic map coordinates. In that case, the two markers are in such close proximity to each other that recombination occurs between them with such low frequency that it is undetectable.
  • Linkage refers to the tendency for alleles to segregate together more often than expected by chance if their transmission was independent. Typically, linkage refers to alleles on the same chromosome. Genetic recombination occurs with an assumed random frequency over the entire genome. Genetic maps are constructed by measuring the frequency of recombination between pairs of traits or markers. The closer the traits or markers are to each other on the chromosome, the lower the frequency of recombination, and the greater the degree of linkage. Traits or markers are considered herein to be linked if they generally co- segregate. A 1/100 probability of recombination per generation is defined as a genetic map distance of 1.0 centiMorgan (1.0 cM).
  • linkage disequilibrium refers to a non-random segregation of genetic loci or traits (or both). In either case, linkage disequilibrium implies that the relevant loci are within sufficient physical proximity along a length of a chromosome so that they segregate together with greater than random (i.e., non-random) frequency. Markers that show linkage disequilibrium are considered linked. Linked loci co-segregate more than 50% of the time, e.g., from about 51 % to about 100% of the time.
  • linkage can be between two markers, or alternatively between a marker and a locus affecting a phenotype.
  • a marker locus can be "associated with” (linked to) a trait. The degree of linkage of a marker locus and a locus affecting a phenotypic trait is measured, e.g., as a statistical probability of co-segregation of that molecular marker with the phenotype (e.g., an F statistic or LOD score).
  • the genetic elements or genes located on a single chromosome segment are physically linked.
  • the two loci are located in close proximity such that recombination between homologous chromosome pairs does not occur between the two loci during meiosis with high frequency, e.g., such that linked loci co-segregate at least about 90% of the time, e.g., 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, 99.75%, or more of the time.
  • the genetic elements located within a chromosomal segment are also "genetically linked", typically within a genetic recombination distance of less than or equal to 50cM, e.g., about 49, 48, 47, 46, 45, 44, 43, 42, 41, 40, 39, 38, 37, 36, 35, 34, 33, 32, 31, 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1, 0.75, 0.5, 0.25 cM or less.
  • two genetic elements within a single chromosomal segment undergo recombination during meiosis with each other at a frequency of less than or equal to about 50%, e.g., about 49%, 48%, 47%, 46%, 45%, 44%, 43%, 42%, 41%, 40%, 39%, 38%, 37%, 36%, 35%, 34%, 33%, 32%, 31%, 30%, 29%, 28%, 27%, 26%, 25%, 24%, 23%, 22%, 21%, 20%, 19%, 18%, 17%, 16%, 15%, 14%, 13%, 12%, 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.75%, 0.5%, 0.25% or less.
  • “Closely linked” markers display a cross over frequency with a given marker of about 10% or less, e.g., 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.75%, 0.5%, 0.25% or less (the given marker locus is within about 10 cM of a closely linked marker locus, e.g., 9, 8, 7, 6, 5, 4, 3, 2, 1, 0.75, 0.5, 0.25 cM or less of a closely linked marker locus).
  • closely linked marker loci co-segregate at least about 90% the time, e.g., 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, 99.75%, or more of the time.
  • introgression refers to both a natural and artificial process whereby chromosomal fragments or genes of one species, variety or cultivar are moved into the genome of another species, variety or cultivar, by crossing those species.
  • the process may optionally be completed by backcrossing to the recurrent parent.
  • introgression of a desired allele at a specified locus can be transmitted to at least one progeny via a sexual cross between two parents of the same species, where at least one of the parents has the desired allele in its genome.
  • transmission of an allele can occur by recombination between two donor genomes, e.g., in a fused protoplast, where at least one of the donor protoplasts has the desired allele in its genome.
  • the desired allele can be, e.g., detected by a marker that is associated with a phenotype, a haplotype, a QTL, a transgene, or the like.
  • offspring comprising the desired allele can be repeatedly backcrossed to a line having a desired genetic background and selected for the desired allele, to result in the allele becoming fixed in a selected genetic background.
  • the process of "introgressing" is often referred to as "backcrossing" when the process is repeated two or more times.
  • “Introgression fragment” or “introgression segment” or “introgression region” refers to a chromosome fragment (or chromosome part or region) which has been introduced into another plant of the same or related species either artificially or naturally such as by crossing or traditional breeding techniques, such as backcrossing, i.e. the introgressed fragment is the result of breeding methods referred to by the verb "to introgress” (such as backcrossing). It is understood that the term “introgression fragment” never includes a whole chromosome, but only a part of a chromosome. The introgression fragment can be large, e.g.
  • a chromosome is preferably smaller, such as about 15 Mb or less, such as about 10 Mb or less, about 9 Mb or less, about 8 Mb or less, about 7 Mb or less, about 6 Mb or less, about 5 Mb or less, about 4 Mb or less, about 3 Mb or less, about 2.5 Mb or 2 Mb or less, about 1 Mb (equals 1,000,000 base pairs) or less, or about 0.5 Mb (equals 500,000 base pairs) or less, such as about 200,000 bp (equals 200 kilo base pairs) or less, about 100,000 bp (100 kb) or less, about 50,000 bp (50 kb) or less, about 25,000 bp (25 kb) or less.
  • a genetic element, an introgression fragment, or a gene or allele conferring a trait (such as increased pathogen resistance or tolerance) is said to be “obtainable from” or can be “obtained from” or “derivable from” or can be “derived from” or “as present in” or “as found in” a plant or plant part as described herein elsewhere if it can be transferred from the plant in which it is present into another plant in which it is not present (such as a line or variety) using traditional breeding techniques without resulting in a phenotypic change of the recipient plant apart from the addition of the trait conferred by the genetic element, locus, introgression fragment, gene or allele.
  • the genetic element, locus, introgression fragment, gene or allele can thus be transferred into any other genetic background lacking the trait.
  • pants comprising the genetic element, locus, introgression fragment, gene or allele can be used, but also progeny/descendants from such plants which have been selected to retain the genetic element, locus, introgression fragment, gene or allele, can be used and are encompassed herein.
  • a plant or genomic DNA, cell or tissue of a plant
  • comprises the same genetic element, locus, introgression fragment, gene or allele as obtainable from such plant can be determined by the skilled person using one or more techniques known in the art, such as phenotypic assays, whole genome sequencing, molecular marker analysis, trait mapping, chromosome painting, allelism tests and the like, or combinations of techniques. It will be understood that transgenic plants may also be encompassed.
  • the polynucleic acid is introduced (and genomically integrated) recombinantly or transgenically.
  • the polynucleic acid may be introduced (and genomically integrated) at the native locus, to replace an endogenous polynucleic acid (such as the polynucleic acid not conferring pathogen resistance), or may be introduced (and genomically integrated) at a locus different than the endogenous locus (e.g. by random integration in the genome).
  • the method for generating a maize plant or plant part comprises transforming a plant or plant part, preferably a plant cell, more preferably a protoplast, with the polynucleic acid, which may be provided on a vector, as described herein elsewhere.
  • the polynucleic acid has a different sequence than an endogenous polynucleic acid (such as an endogenous polynucleic acid not conferring pathogen resistance).
  • genetic engineering As used herein the terms “genetic engineering”, “transformation” and “genetic modification” are all used herein as synonyms for the transfer of isolated and cloned genes into the DNA, usually the chromosomal DNA or genome, of another organism.
  • Transgenic or “genetically modified organisms” as used herein are organisms whose genetic material has been altered using techniques generally known as “recombinant DNA technology”.
  • Recombinant DNA technology encompasses the ability to combine DNA molecules from different sources into one molecule ex vivo (e.g. in a test tube).
  • the term “transgenic” here means genetically modified by the introduction of a non-endogenous nucleic acid sequence. Typically a species-specific nucleic acid sequence is introduced in a form, arrangement or quantity into the cell in a location where the nucleic acid sequence does not occur naturally in the cell.
  • Non-transgenic refers to plants and food products derived from plants that are not “transgenic” or “genetically modified organisms” as defined above.
  • Transgene or “chimeric gene” refers to a genetic locus comprising a DNA sequence, such as a recombinant gene, which has been introduced into the genome of a plant by transformation, such as Agrobacterium mediated transformation.
  • a plant comprising a transgene stably integrated into its genome is referred to as "transgenic plant”.
  • Gene editing refers to genetic engineering in which in which DNA or RNA is inserted, deleted, modified or replaced in the genome of a living organism. Gene editing may comprise targeted or non-targeted (random) mutagenesis. Targeted mutagenesis may be accomplished for instance with designer nucleases, such as for instance with meganucleases, zinc finger nucleases (ZFNs), transcription activator-like effector-based nucleases (TALEN), and the clustered regularly interspaced short palindromic repeats (CRISPR/Cas9) system. These nucleases create site-specific double-strand breaks (DSBs) at desired locations in the genome.
  • ZFNs zinc finger nucleases
  • TALEN transcription activator-like effector-based nucleases
  • CRISPR/Cas9 clustered regularly interspaced short palindromic repeats
  • the induced double-strand breaks are repaired through nonhomologous end-joining (NHEJ) or homologous recombination (HR), resulting in targeted mutations or nucleic acid modifications.
  • NHEJ nonhomologous end-joining
  • HR homologous recombination
  • designer nucleases is particularly suitable for generating gene knockouts or knockdowns.
  • designer nucleases are developed which specifically introduce one or more of the molecular marker (allele) according to the invention as described herein. Delivery and expression systems of designer nuclease systems are well known in the art.
  • the nuclease or targeted/site-specific/homing nuclease is, comprises, consists essentially of, or consists of a (modified) CRISPR/Cas system or complex, a (modified) Cas protein, a (modified) zinc finger, a (modified) zinc finger nuclease (ZFN), a (modified) transcription factor-like effector (TALE), a (modified) transcription factor-like effector nuclease (TALEN), or a (modified) meganuclease.
  • said (modified) nuclease or targeted/site-specific/homing nuclease is, comprises, consists essentially of, or consists of a (modified) RNA-guided nuclease.
  • the nucleases may be codon optimized for expression in plants.
  • targeting of a selected nucleic acid sequence means that a nuclease or nuclease complex is acting in a nucleotide sequence specific manner.
  • the guide RNA is capable of hybridizing with a selected nucleic acid sequence.
  • hybridization or “hybridizing” refers to a reaction in which one or more polynucleotides react to form a complex that is stabilized via hydrogen bonding between the bases of the nucleotide residues, i.e. a process in which a single-stranded nucleic acid molecule attaches itself to a complementary nucleic acid strand, i.e. agrees with this base pairing.
  • Standard procedures for hybridization are described, for example, in Sambrook et al. (Molecular Cloning. A Laboratory Manual, Cold Spring Harbor Laboratory Press, 3rd edition 2001 ).
  • the hydrogen bonding may occur by Watson Crick base pairing, Hoogstein binding, or in any other sequence specific manner.
  • the complex may comprise two strands forming a duplex structure, three or more strands forming a multi stranded complex, a single self-hybridizing strand, or any combination of these.
  • a hybridization reaction may constitute a step in a more extensive process, such as the initiation of PGR, or the cleavage of a polynucleotide by an enzyme.
  • a sequence capable of hybridizing with a given sequence is referred to as the "complement" of the given sequence.
  • this will be understood to mean an at least 50%, more preferably at least 55%, 60%, 65%, 70%, 75%, 80% or 85%, more preferably 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% of the bases of the nucleic acid strand form base pairs with the complementary nucleic acid strand.
  • the possibility of such binding depends on the stringency of the hybridization conditions.
  • Gene editing may involve transient, inducible, or constitutive expression of the gene editing components or systems. Gene editing may involve genomic integration or episomal presence of the gene editing components or systems. Gene editing components or systems may be provided on vectors, such as plasmids, which may be delivered by appropriate delivery vehicles, as is known in the art. Preferred vectors are expression vectors.
  • Gene editing may comprise the provision of recombination templates, to effect homology directed repair (HDR).
  • HDR homology directed repair
  • a genetic element may be replaced by gene editing in which a recombination template is provided.
  • the DNA may be cut upstream and downstream of a sequence which needs to be replaced.
  • the sequence to be replaced is excised from the DNA.
  • the marker (allele) of the invention as described herein may be provided on/as a template.
  • the polynucleic acid of the invention may be provided on/as a template. More advantageously however, the polynucleic acid of the invention may be generated without the use of a recombination template, but solely through the endonuclease action leading to a double strand DNA break which is repaired by NHEJ, resulting in the generation of indels.
  • the nucleic acid modification is effected by random mutagenesis.
  • Cells or organisms may be exposed to mutagens such as UV radiation or mutagenic chemicals (such as for instance such as ethyl methanesulfonate (EMS)), and mutants with desired characteristics are then selected.
  • Mutants can for instance be identified by TILLING (Targeting Induced Local Lesions in Genomes).
  • TILLING Targeting Induced Local Lesions in Genomes.
  • the method combines mutagenesis, such as mutagenesis using a chemical mutagen such as ethyl methanesulfonate (EMS) with a sensitive DNA screening-technique that identifies single base mutations/point mutations in a target gene.
  • EMS ethyl methanesulfonate
  • the TILLING method relies on the formation of DNA heteroduplexes that are formed when multiple alleles are amplified by PCR and are then heated and slowly cooled. A "bubble” forms at the mismatch of the two DNA strands, which is then cleaved by a single stranded nucleases. The products are then separated by size, such as by HPLC. See also McCallum et al. "Targeted screening for induced mutations"; Nat Biotechnol. 2000 Apr;18(4):455-7 and McCallum et al. "Targeting induced local lesions IN genomes (TILLING) for plant functional genomics"; Plant Physiol. 2000 Jun; 123(2):439-42 .
  • the term “homozygote” refers to an individual cell or plant having the same alleles at one or more or all loci. When the term is used with reference to a specific locus or gene, it means at least that locus or gene has the same alleles. As used herein, the term “homozygous” means a genetic condition existing when identical alleles reside at corresponding loci on homologous chromosomes. As used herein, the term “heterozygote” refers to an individual cell or plant having different alleles at one or more or all loci. When the term is used with reference to a specific locus or gene, it means at least that locus or gene has different alleles.
  • the term "heterozygous” means a genetic condition existing when different alleles reside at corresponding loci on homologous chromosomes.
  • the haplotype and/or one or more marker(s) as described herein is/are homozygous.
  • the haplotype and/or one or more marker(s) as described herein are heterozygous.
  • the haplotype allele and/or one or more marker(s) allele(s) as described herein is/are homozygous.
  • the haplotype allele and/or one or more marker(s) allele(s) as described herein are heterozygous.
  • sequence identity refers to the degree of identity between any given nucleic acid sequence and a target nucleic acid sequence. Percent sequence identity is calculated by determining the number of matched positions in aligned nucleic acid sequences, dividing the number of matched positions by the total number of aligned nucleotides, and multiplying by 100. A matched position refers to a position in which identical nucleotides occur at the same position in aligned nucleic acid sequences. Percent sequence identity also can be determined for any amino acid sequence.
  • a target nucleic acid or amino acid sequence is compared to the identified nucleic acid or amino acid sequence using the BLAST 2 Sequences (BI2seq) program from the stand-alone version of BLASTZ containing BLASTN and BLASTP.
  • This stand-alone version of BLASTZ can be obtained from Fish & Richardson's web site (World Wide Web at fr.com/blast) or the U.S. government's National Center for Biotechnology Information web site (World Wide Web at ncbi.nlm.nih.gov). Instructions explaining how to use the BI2seq program can be found in the readme file accompanying BLASTZ.
  • BI2seq performs a comparison between two sequences using either the BLASTN or BLASTP algorithm.
  • BLASTN is used to compare nucleic acid sequences
  • BLASTP is used to compare amino acid sequences.
  • the options are set as follows: -i is set to a file containing the first nucleic acid sequence to be compared (e.g. , C: ⁇ seq I .txt); -j is set to a file containing the second nucleic acid sequence to be compared (e.g. , C: ⁇ seq2.txt); -p is set to blastn; -o is set to any desired file name (e.g.
  • C ⁇ output.txt
  • -q is set to - 1
  • -r is set to 2; and all other options are left at their default setting.
  • the following command will generate an output file containing a comparison between two sequences: C: ⁇ B12seq -i c: ⁇ seql .txt -j c: ⁇ seq2.txt -p blastn -o c: ⁇ output.txt -q - 1 -r 2. If the target sequence shares homology with any portion of the identified sequence, then the designated output file will present those regions of homology as aligned sequences. If the target sequence does not share homology with any portion of the identified sequence, then the designated output file will not present aligned sequences.
  • a length is determined by counting the number of consecutive nucleotides from the target sequence presented in alignment with the sequence from the identified sequence starting with any matched position and ending with any other matched position.
  • a matched position is any position where an identical nucleotide is presented in both the target and identified sequences. Gaps presented in the target sequence are not counted since gaps are not nucleotides. Likewise, gaps presented in the identified sequence are not counted since target sequence nucleotides are counted, not nucleotides from the identified sequence.
  • the percent identity over a particular length is determined by counting the number of matched positions over that length and dividing that number by the length followed by multiplying the resulting value by 100.
  • 78.11, 78.12, 78.13, and 78.14 are rounded down to 78.1
  • 78.15, 78.16, 78.17, 78.18, and 78.19 are rounded up to 78.2.
  • the length value will always be an integer.
  • sequence when used herein relates to nucleotide sequence(s), polynucleotide(s), nucleic acid sequence(s), nucleic acid(s), nucleic acid molecule, peptides, polypeptides and proteins, depending on the context in which the term “sequence” is used.
  • nucleotide sequence(s) refers to nucleotides, either ribonucleotides or deoxyribonucleotides or a combination of both, in a polymeric unbranched form of any length.
  • Nucleic acid sequences include DNA, cDNA, genomic DNA, RNA, synthetic forms and mixed polymers, both sense and antisense strands, or may contain non-natural or derivatized nucleotide bases, as will be readily appreciated by those skilled in the art.
  • isolated nucleic acid sequence refers to a nucleic acid sequence which is no longer in the natural environment from which it was isolated, e.g. the nucleic acid sequence in a bacterial host cell or in the plant nuclear or plastid genome.
  • sequence When referring to a “sequence” herein, it is understood that the molecule having such a sequence is referred to, e.g. the nucleic acid molecule.
  • a "host cell” or a “recombinant host cell” or “transformed cell” are terms referring to a new individual cell (or organism) arising as a result of at least one nucleic acid molecule, having been introduced into said cell.
  • the host cell is preferably a plant cell or a bacterial cell.
  • the host cell may contain the nucleic acid as an extra-chromosomally (episomal) replicating molecule, or comprises the nucleic acid integrated in the nuclear or plastid genome of the host cell, or as introduced chromosome, e.g. minichromosome.
  • nucleic acid sequence e.g. DNA or genomic DNA
  • nucleic acid sequence identity to a reference sequence or having a sequence identity of at least 80%>, e.g. at least 85%, 90%, 95%, 98%> or 99%> nucleic acid sequence identity to a reference sequence
  • said nucleotide sequence is considered substantially identical to the given nucleotide sequence and can be identified using stringent hybridisation conditions.
  • the nucleic acid sequence comprises one or more mutations compared to the given nucleotide sequence but still can be identified using stringent hybridisation conditions.
  • Stringent hybridisation conditions can be used to identify nucleotide sequences, which are substantially identical to a given nucleotide sequence.
  • Stringent conditions are sequence dependent and will be different in different circumstances. Generally, stringent conditions are selected to be about 5°C lower than the thermal melting point (Tm) for the specific sequences at a defined ionic strength and pH. The Tm is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridises to a perfectly matched probe. Typically stringent conditions will be chosen in which the salt concentration is about 0.02 molar at pH 7 and the temperature is at least 60°C. Lowering the salt concentration and/or increasing the temperature increases stringency. Stringent conditions for RNA-DNA hybridisations (Northern blots using a probe of e.g.
  • 100 nt are for example those which include at least one wash in 0.2X SSC at 63°C for 20min, or equivalent conditions.
  • Stringent conditions for DNA-DNA hybridisation are for example those which include at least one wash (usually 2) in 0.2X SSC at a temperature of at least 50°C, usually about 55°C, for 20 min, or equivalent conditions. See also Sambrook et al. (1989) and Sambrook and Russell (2001).
  • polypeptide or "protein” (both terms are used interchangeably herein) means a peptide, a protein, or a polypeptide which encompasses amino acid chains of a given length, wherein the amino acid residues are linked by covalent peptide bonds.
  • peptidomimetics of such proteins/polypeptides wherein amino acid(s) and/or peptide bond(s) have been replaced by functional analogs are also encompassed by the invention as well as other than the 20 gene-encoded amino acids, such as selenocysteine.
  • Peptides, oligopeptides and proteins may be termed polypeptides.
  • polypeptide also refers to, and does not exclude, modifications of the polypeptide, e.g., glycosylation, acetylation, phosphorylation and the like. Such modifications are well described in basic texts and in more detailed monographs, as well as in the research literature.
  • Amino acid substitutions encompass amino acid alterations in which an amino acid is replaced with a different naturally-occurring amino acid residue. Such substitutions may be classified as "conservative ⁇ 1>, in which an amino acid residue contained in the wild-type protein is replaced with another naturally-occurring amino acid of similar character, for example Gly ⁇ ->Ala, Val ⁇ ->Ile ⁇ ->Leu, Asp ⁇ ->Glu, Lys ⁇ ->Arg, Asn ⁇ ->Gln or Phe ⁇ ->Trp ⁇ ->Tyr.
  • substitutions encompassed by the present invention may also be "non-conservative", in which an amino acid residue which is present in the wild-type protein is substituted with an amino acid with different properties, such as a naturally-occurring amino acid from a different group (e.g. substituting a charged or hydrophobic amino acid with alanine.
  • Similar amino acids refers to amino acids that have similar amino acid side chains, i.e. amino acids that have polar, non-polar or practically neutral side chains.
  • Non-similar amino acids refers to amino acids that have different amino acid side chains, for example an amino acid with a polar side chain is non-similar to an amino acid with a non-polar side chain.
  • Polar side chains usually tend to be present on the surface of a protein where they can interact with the aqueous environment found in cells ("hydrophilic” amino acids).
  • non-polar amino acids tend to reside within the center of the protein where they can interact with similar non-polar neighbours (“hydrophobic” amino acids”).
  • amino acids that have polar side chains are arginine, asparagine, aspartate, cysteine, glutamine, glutamate, histidine, lysine, serine, and threonine (all hydrophilic, except for cysteine which is hydrophobic).
  • amino acids that have non-polar side chains are alanine, glycine, isoleucine, leucine, methionine, phenylalanine, proline, and tryptophan (all hydrophobic, except for glycine which is neutral).
  • a gene when used herein refers to a polymeric form of nucleotides of any length, either ribonucleotides or desoxyribonucleotides.
  • the term includes double- and single-stranded DNA and RNA. It also includes known types of modifications, for example, methylation, "caps", substitutions of one or more of the naturally occurring nucleotides with an analog.
  • a gene comprises a coding sequence encoding the herein defined polypeptide.
  • a "coding sequence” is a nucleotide sequence which is transcribed into mRNA and/or translated into a polypeptide when placed or being under the control of appropriate regulatory sequences.
  • a coding sequence can include, but is not limited to mRNA, cDNA, recombinant nucleic acid sequences or genomic DNA, while introns may be present as well under certain circumstances.
  • the term “endogenous” refers to a gene or allele which is present in its natural genomic location.
  • the term “endogenous” can be used interchangeably with “native”. This does not however exclude the presence of one or more nucleic acid differences with the wild-type allele.
  • the difference with a wild-type allele can be limited to less than 9 preferably less than 6, more particularly less than 3 nucleotide differences, such as 0 nucleotides difference. More particularly, the difference with the wildtype sequence can be in only one nucleotide.
  • the endogenous allele encodes a modified protein having less than 9, preferably less than 6, more particularly less than 3 and even more preferably only one or no amino acid difference with the wild-type protein.
  • exogenous polynucleotide refers to a polynucleotide, such as a gene (or cDNA) or allele which is or has been recombinantly introduced in a cell (or plant).
  • the exogenous polynucleotide may be episomal or genomically integrated. Integration may be random or site-directed. Integration may include replacement of a corresponding endogenous polynucleotide. It will be understood that an exogenous polynucleotide is not naturally present in the cell or plant.
  • the B73 reference genome AGPv4 refers to the assembly B73 RefGen_v4 (also known as AGPv4, B73 RefGen_v4) as provided on the Maize Genetics and Genomics Database (https://www.maizegdb.org/genome/genome_assembly/Zm-B73-REFERENCE-GRAMEN E-4.0).
  • screening may encompass or comprise sequencing, hybridization based methods (such as (dynamic) allele-specific hybridization, molecular beacons, SNP microarrays), enzyme based methods (such as PCR, KASP (Kompetitive Allele Specific PCR), RFLP, ALFP, RAPD, Flap endonuclease, primer extension, 5'-nuclease, oligonucleotide ligation assay), post-amplification methods based on physical properties of DNA (such as single strand conformation polymorphism, temperature gradient gel electrophoresis, denaturing high performance liquid chromatography, high-resolution melting of the entire amplicon, use of DNA mismatch-binding proteins, SNPlex, surveyor nuclease assay), etc.
  • hybridization based methods such as (dynamic) allele-specific hybridization, molecular beacons, SNP microarrays
  • enzyme based methods such as PCR, KASP (Kompetitive Allele Specific PCR), RFLP, ALFP, RA
  • the invention relates to a method for identifying a plant, plant part or plant material, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying a cytoplasmic male sterility restorer locus on chromosome 3, in particular RF-03-01, as described herein elsewhere.
  • the invention relates to a method for identifying a plant, plant part or plant material, in particular a maize plant or plant part, comprising screening for the absence of a cytoplasmic male sterility restorer locus on chromosome 3, in particular RF-03-01, as described herein elsewhere.
  • the invention relates to a method for identifying a plant, plant part or plant material, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying a cytoplasmic male sterility maintainer locus on chromosome 3, in particular RF-03-01, as described herein elsewhere.
  • the invention relates to a method for identifying a plant, plant part or plant material, in particular a maize plant or plant part, comprising screening for the absence of a cytoplasmic male sterility maintainer locus on chromosome 3, in particular RF-03-01, as described herein elsewhere.
  • the invention relates to a method for identifying a plant, plant part or plant material, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying (a haplotype associated with/linked) with a cytoplasmic male sterility restorer locus on chromosome 3, in particular RF-03-01, as described herein elsewhere.
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the absence of (a haplotype associated with/linked with) a cytoplasmic male sterility restorer locus on chromosome 3, in particular RF-03-01, as described herein elsewhere.
  • the invention relates to a method for identifying a plant, plant part or plant material, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying (a haplotype associated with/linked with) a cytoplasmic male sterility maintainer locus on chromosome 3, in particular RF-03-01, as described herein elsewhere.
  • the invention relates to a method for identifying a plant, plant part or plant material, in particular a maize plant or plant part, comprising screening for the absence of (a haplotype associated with/linked with) a cytoplasmic male sterility maintainer locus on chromosome 3, in particular RF-03-01, as described herein elsewhere.
  • the invention relates to a method for identifying a plant, plant part or plant material, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying one or more molecular markers of Table 4 or Table 5.
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying two or more molecular markers of Table 4 or Table 5.
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying three or more molecular markers of Table 4 or Table 5.
  • the method is a method for identifying a plant or plant part comprising a cytoplasmic male sterility restorer locus. In certain embodiments, the method is a method for identifying a plant or plant part comprising a cytoplasmic male sterility maintainer locus.
  • the invention relates to a method for identifying a plant, plant part or plant material, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying one or more molecular marker alleles of Table 4 or Table 5 (and having a polymorphism corresponding to or comprised in a cytoplasmic male sterility restorer locus).
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying two or more molecular marker alleles of Table 4 or Table 5 (and having a polymorphism corresponding to or comprised in a cytoplasmic male sterility restorer locus).
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying three or more molecular marker alleles of Table 4 or Table 5 (and having a polymorphism corresponding to or comprised in a cytoplasmic male sterility restorer locus).
  • the invention relates to a method for identifying a plant, plant part or plant material, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying one or more molecular marker alleles of Table 4 or Table 5 (and having a polymorphism corresponding to or comprised in a cytoplasmic male sterility maintainer locus).
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying two or more molecular marker alleles of Table 4 or Table 5 (and having a polymorphism corresponding to or comprised in a cytoplasmic male sterility maintainer locus).
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying three or more molecular marker alleles of Table 4 or Table 5 (and having a polymorphism corresponding to or comprised in a cytoplasmic male sterility maintainer locus).
  • the invention relates to a method for identifying a plant, plant part or plant material, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying one or more polynucleic acid sequences having a sequence as set forth in any of SEQ ID NOs: 1, 5, 9, 13, 2, 6, 10, or 14.
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying two or more polynucleic acid sequences having a sequence as set forth in any of SEQ ID NOs: 1, 5, 9, 13, 2, 6, 10, or 14.
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying three or more polynucleic acid sequences having a sequence as set forth in any of SEQ ID NOs: 1, 5, 9, 13, 2, 6, 10, or 14.
  • the method is a method for identifying a plant or plant part comprising a cytoplasmic male sterility restorer locus.
  • the method is a method for identifying a plant or plant part comprising a cytoplasmic male sterility maintainer locus.
  • the invention relates to a method for identifying a plant, plant part or plant material, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying one or more polynucleic acid sequences having a sequence as set forth in any of SEQ ID NOs: 1, 5, 9, or 13.
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying two or more polynucleic acid sequences having a sequence as set forth in any of SEQ ID NOs: 1, 5, 9, or 13.
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying three or more polynucleic acid sequences having a sequence as set forth in any of SEQ ID NOs: 1, 5, 9, or 13.
  • the method is a method for identifying a plant or plant part comprising a cytoplasmic male sterility restorer locus.
  • the invention relates to a method for identifying a plant, plant part or plant material, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying one or more polynucleic acid sequences having a sequence as set forth in any of SEQ ID NOs: 2, 6, 10, or 14.
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying two or more polynucleic acid sequences having a sequence as set forth in any ofSEQ ID NOs: 2, 6, 10, or 14.
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying three or more polynucleic acid sequences having a sequence as set forth in any of SEQ ID NOs: 2, 6, 10, or 14.
  • the method is a method for identifying a plant or plant part comprising a cytoplasmic male sterility maintainer locus.
  • the invention relates to a method for identifying a plant, plant part or plant material, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying one or more genes selected from Zm00001d043358, Zm00001d043352, Zm00001d043356, and Zm00001d043357 having respectively a coding sequence as set forth in any of SEQ ID NOs: 201, 203, 205, 207, 3, 7, 11, or 15.
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying two or more genes selected from Zm00001d043358, Zm00001d043352, Zm00001d043356, and Zm00001d043357 having respectively a coding sequence as set forth in any of SEQ ID NOs: 201, 203, 205, 207, 3, 7, 11, or 15.
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying three or more genes selected from Zm00001d043358, Zm00001d043352, Zm00001d043356, and Zm00001d043357 having respectively a coding sequence as set forth in any of SEQ ID NOs: 201, 203, 205, 207, 3, 7, 11, or 15.
  • the method is a method for identifying a plant or plant part comprising a cytoplasmic male sterility restorer locus.
  • the method is a method for identifying a plant or plant part comprising a cytoplasmic male sterility maintainer locus.
  • the invention relates to a method for identifying a plant, plant part or plant material, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying one or more genes selected from Zm00001d043358, Zm00001d043352, Zm00001d043356, and Zm00001d043357 having respectively a coding sequence as set forth in any of SEQ ID NOs: 201, 203, 205, or 207.
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying two or more genes selected from Zm00001d043358, Zm00001d043352, Zm00001d043356, and Zm00001d043357 having respectively a coding sequence as set forth in any of SEQ ID NOs: 201, 203, 205, or 207.
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying three or more genes selected from Zm00001d043358, Zm00001d043352, Zm00001d043356, and Zm00001d043357 having respectively a coding sequence as set forth in any of SEQ ID NOs: 201, 203, 205, or 207.
  • the method is a method for identifying a plant or plant part comprising a cytoplasmic male sterility restorer locus.
  • the invention relates to a method for identifying a plant, plant part or plant material, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying one or more genes selected from Zm00001d043358, Zm00001d043352, Zm00001d043356, and Zm00001d043357 having respectively a coding sequence as set forth in any of SEQ ID NOs: 3, 7, 11, or 15.
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying two or more genes selected from Zm00001d043358, Zm00001d043352, Zm00001d043356, and Zm00001d043357 having respectively a coding sequence as set forth in any of SEQ ID NOs: 3, 7, 11, or 15.
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying three or more genes selected from Zm00001d043358, Zm00001d043352, Zm00001d043356, and Zm00001d043357 having respectively a coding sequence as set forth in any of SEQ ID NOs: 3, 7, 11, or 15.
  • the method is a method for identifying a plant or plant part comprising a cytoplasmic male sterility maintainer locus.
  • the invention relates to a method for identifying a plant, plant part or plant material, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying one or more genes selected from Zm00001d043358, Zm00001d043352, Zm00001d043356, and Zm00001d043357 encoding respectively a polypeptide having a sequence as set forth in any of SEQ ID NOs: 202, 204, 206, 208, 4, 8, 12, or 16.
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying two or more genes selected from Zm00001d043358, Zm00001d043352, Zm00001d043356, and Zm00001d043357 encoding respectively a polypeptide having a sequence as set forth in any of SEQ ID NOs: 202, 204, 206, 208, 4, 8, 12, or 16.
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying three or more genes selected from Zm00001d043358, Zm00001d043352, Zm00001d043356, and Zm00001d043357 encoding respectively a polypeptide having a sequence as set forth in any of SEQ ID NOs: 202, 204, 206, 208, 4, 8, 12, or 16.
  • the method is a method for identifying a plant or plant part comprising a cytoplasmic male sterility restorer locus.
  • the method is a method for identifying a plant or plant part comprising a cytoplasmic male sterility maintainer locus.
  • the invention relates to a method for identifying a plant, plant part or plant material, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying one or more genes selected from Zm00001d043358, Zm00001d043352, Zm00001d043356, and Zm00001d043357 encoding respectively a polypeptide having a sequence as set forth in any of SEQ ID NOs: 202, 204, 206, or 208, preferably selected from Zm00001d043358, Zm00001d043352, and Zm00001d043357 encoding respectively a polypeptide having a sequence as set forth in any of SEQ ID NOs: 202, 204, or 208.
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying two or more genes selected from Zm00001d043358, Zm00001d043352, Zm00001d043356, and Zm00001d043357 encoding respectively a polypeptide having a sequence as set forth in any of SEQ ID NOs: 202, 204, 206, or 208, preferably selected from Zm00001d043358, Zm00001d043352, and Zm00001d043357 encoding respectively a polypeptide having a sequence as set forth in any of SEQ ID NOs: 202, 204, or 208.
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying three or more genes selected from Zm00001d043358, Zm00001d043352, Zm00001d043356, and Zm00001d043357 encoding respectively a polypeptide having a sequence as set forth in any of SEQ ID NOs: 202, 204, 206, or 208, preferably selected from Zm00001d043358, Zm00001d043352, and Zm00001d043357 encoding respectively a polypeptide having a sequence as set forth in any of SEQ ID NOs: 202, 204, or 208.
  • the method is a method for identifying a plant or plant part comprising a cytoplasmic male sterility restorer locus.
  • the invention relates to a method for identifying a plant, plant part or plant material, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying one or more genes selected from Zm00001d043358, Zm00001d043352, and Zm00001d043357 encoding respectively a polypeptide having a sequence as set forth in any of SEQ ID NOs: 4, 8, or 16.
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying two or more genes selected from Zm00001d043358, Zm00001d043352, and Zm00001d043357 encoding respectively a polypeptide having a sequence as set forth in any of SEQ ID NOs: 4, 8, or 16.
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying three or more genes selected from Zm00001d043358, Zm00001d043352, and Zm00001d043357 encoding respectively a polypeptide having a sequence as set forth in any of SEQ ID NOs: 4, 8, or 16.
  • the method is a method for identifying a plant or plant part comprising a cytoplasmic male sterility maintainer locus.
  • the invention relates to a method for identifying a plant, plant part or plant material, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying one or more polynucleic acid sequences having a sequence as set forth in any of SEQ ID NOs: 17 to 200.
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying two or more polynucleic acid sequences having a sequence as set forth in any of SEQ ID NOs: 17 to 200.
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying three or more polynucleic acid sequences having a sequence as set forth in any of SEQ ID NOs: 17 to 200.
  • the invention relates to a method for identifying a plant, plant part or plant material, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying one or more polynucleic acid sequences having a sequence as set forth in any of SEQ ID NOs: 17 to 200 and having a polymorphism corresponding to a cytoplasmic male sterility restorer locus.
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying two or more polynucleic acid sequences having a sequence as set forth in any of SEQ ID NOs: 17 to 200 and having a polymorphism corresponding to a cytoplasmic male sterility restorer locus.
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying three or more polynucleic acid sequences having a sequence as set forth in any of SEQ ID NOs: 17 to 200 and having a polymorphism corresponding to a cytoplasmic male sterility restorer locus.
  • the invention relates to a method for identifying a plant, plant part or plant material, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying one or more polynucleic acid sequences having a sequence as set forth in any of SEQ ID NOs: 17 to 200 and having a polymorphism not corresponding to a cytoplasmic male sterility maintainer locus.
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying two or more polynucleic acid sequences having a sequence as set forth in any of SEQ ID NOs: 17 to 200 and having a polymorphism not corresponding to a cytoplasmic male sterility maintainer locus.
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying three or more polynucleic acid sequences having a sequence as set forth in any of SEQ ID NOs: 17 to 200 and having a polymorphism not corresponding to a cytoplasmic male sterility maintainer locus.
  • the invention relates to a method for identifying a plant, plant part or plant material, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying one or more, two or more, or three or more of the following polymorphisms (positions correspond to maize reference B73 AGPv4 chromosome 3): Position AGPv4 polymorphism maintainer restorer 195629901 ade gua 195639694 thy cyt 195677799 gua ade 195678356 cyt gua 195680790 gua ade 195732936 gua ade 195733916 cyt ade 195783701 cyt thy 196070086 cyt thy 196198736 ade gua 196244714 thy cyt 196653746 cyt thy 196693501 cyt ade 196702811 ade gua 196704008 ade
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying a polymorphism at a position corresponding to maize reference B73 AGPv4 chromosome 3 position 195629901.
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying a SNP at a position corresponding to maize reference B73 AGPv4 chromosome 3 position 195629901.
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying a SNP at a position corresponding to maize reference B73 AGPv4 chromosome 3 position 195629901, wherein if a G is detected, said maize plant or plant part is a restorer or comprises a restorer (gene(s), locus, haplotype, genome, or phenotype), in particular the restorer of the invention.
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying a SNP at a position corresponding to maize reference B73 AGPv4 chromosome 3 position 195629901,wherein if a nucleotide other than G is detected, said maize plant or plant part is a not a restorer or does not comprise a restorer (gene(s), locus, haplotype, genome, or phenotype), in particular the restorer of the invention.
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying a SNP at a position corresponding to maize reference B73 AGPv4 chromosome 3 position 195629901,wherein if a nucleotide other than G is detected, said maize plant or plant part is a maintainer or comprise a maintainer (gene(s), locus, haplotype, genome, or phenotype), in particular the maintainer of the invention.
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying a SNP at a position corresponding to maize reference B73 AGPv4 chromosome 3 position 195629901,wherein if a nucleotide A is detected, said maize plant or plant part is a not a restorer or does not comprise a restorer (gene(s), locus, haplotype, genome, or phenotype), in particular the restorer of the invention.
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying a SNP at a position corresponding to maize reference B73 AGPv4 chromosome 3 position 195629901,wherein if a nucleotide A is detected, said maize plant or plant part is a maintainer or comprise a maintainer (gene(s), locus, haplotype, genome, or phenotype), in particular the maintainer of the invention.
  • the indicated nucleotide positions are the nucleotide positions of the indicated AGPv04 B73 chromosome 3 positions and that the marker positions in the maize plants according to the invention correspond to the indicated marker positions, but are or comprise not necessarily identical positions in a different genome (e.g. from a different race or line).
  • corresponding nucleotide positions can be determined by suitable alignment, as is known in the art.
  • the nucleotides (SNPs) at the positions indicated for the restorer allele allow screening for or the identification of the restorer phenotype according to the invention.
  • the nucleotides (SNPs) at the positions indicated for the maintainer allele allow screening for or the identification of the non-restorer phenotype (i.e. the restorer locus at maize chromosome is not present). It will be understood that for identification of the non-restorer allele the indicated SNP nucleotides may be different than those indicated in the Table (as long as these are different than the SNP nucleotides indicated for the restorer allele).
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying one or more, two or more, or three or more of the following polymorphisms (positions correspond to the indicated positions of the respective SEQ ID NOs): SEQ ID NO: Position B73 (AGPv4) SEQ ID NO: Position restorer polymorphism maintainer restorer 1 35 2 35 g t 1 404 2 404 t c 1 444-452 2 443-444 gggactttc Deletion 1 463 2 454 c t 1 537 2 528 g c 1 735 2 726 g a 1 748-759 2 738-739 tactttgtaaca Deletion 1 761 2 740 t a 1 797 2 776 a g 1 1048 2 1027 g t 1 1056 2 1035 a c 1 1065-1066 2 1045 tc Insert
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying a polymorphism at a position corresponding to position 35 of SEQ ID NO: 1.
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying a polymorphism at a position corresponding to position 35 of SEQ ID NO: 2.
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying a polymorphism at a position corresponding to position 35 of SEQ ID NO: 1, wherein if a G is detected said maize plant or plant part is a maintainer or is not a restorer or comprises a maintainer (gene(s), locus, haplotype, genome, or phenotype) or does not comprise a restorer (gene(s), locus, haplotype, genome, or phenotype), in particular the maintainer/restorer of the invention.
  • the invention relates to a method for identifying a plant or plant part, in particular a maize plant or plant part, comprising screening for the presence of or detecting or identifying a polymorphism at a position corresponding to position 35 of SEQ ID NO: 2, wherein if a T is detected said maize plant or plant part is restorer or comprises a restorer (gene(s), locus, haplotype, genome, or phenotype), in particular the restorer of the invention.
  • a restorer gene(s), locus, haplotype, genome, or phenotype
  • KASP primers may for instance be developed to discriminate between the restorer and non-restorer/maintainer polymorphisms.
  • the methods for identifying a (maize) plant or plant part as described herein may comprise screening of a sample obtained from a (maize) plant or plant part, in particular a sample comprising genomic DNA of the (maize) plant or plant part. Accordingly, the method may comprise the step of obtaining a sample (comprising genomic DNA) from a (maize) plant or plant part, or providing a sample (comprising genomic DNA) obtained from a (maize) plant or plant part.
  • Methods for screening or identifying markers are well known in the art, as also described herein elsewhere.
  • the methods for identifying a (maize) plant or plant part as described herein allow for discriminating between plants or plant parts having a cytoplasmic male sterility restorer or a cytoplasmic male sterility maintainer genotype, haplotype, and/or phenotype based on the identity of the polymorphisms or polymorphic alleles described herein.
  • the molecular marker(s) (allele(s)) of the present invention can be advantageously used to identify maize plants as being a restorer or having a restorer gene, locus (allele), haplotype, genotype or phenotype or as not being a restorer or not having a restorer gene, locus (allele), haplotype, genotype or phenotype, in particular the restorer of the invention.
  • such plants or plant parts may nevertheless comprise other restorer genes or loci.
  • the methods for identifying plants or plant parts as described herein can be methods for identifying plants or plant parts comprising said CMS restorer locus or alternatively methods for identifying plants or plant parts not comprising said CMS restorer locus.
  • Such identification can be based on the polymorphisms described herein, in particular the polymorphic alleles associated with/linked with the restorer locus or alternatively the polymorphic alleles associated with/linked with the maintainer locus.
  • the methods for identifying plants or plant parts as described herein can be methods for identifying plants or plant parts comprising the CMS maintainer locus or alternatively methods for identifying plants or plant parts not comprising the CMS maintainer locus.
  • the restorer locus of the invention is comprised on maize chromosome 3 in a genomic interval corresponding to (nucleic acid) position 195629901 to 198023573 of the B73 reference maize genome AGPv4, or a fragment thereof.
  • the restorer locus comprises on maize chromosome 3 a genomic interval corresponding to (nucleic acid) position 195629901 to 198023573 of the B73 reference maize genome AGPv4, or a fragment thereof.
  • the restorer locus is flanked on maize chromosome 3 by (nucleic acid) positions corresponding to positions 195629901 and 198023573 of the B73 reference maize genome AGPv4, or a fragment thereof.
  • the restorer locus of the invention is comprised on maize chromosome 3 in a genomic interval corresponding to (nucleic acid) position 197453646 to 197698278 of the B73 reference maize genome AGPv4, or a fragment thereof.
  • the restorer locus comprises on maize chromosome 3 a genomic interval corresponding to (nucleic acid) position 197453646 to 197698278 of the B73 reference maize genome AGPv4, or a fragment thereof.
  • the restorer locus is flanked on maize chromosome 3 by (nucleic acid) positions corresponding to positions 197453646 and 197698278 of the B73 reference maize genome AGPv4, or a fragment thereof.
  • the restorer locus of the invention is comprised on maize chromosome 3 in a genomic interval corresponding to (nucleic acid) position 195629901 to 197698278 of the B73 reference maize genome AGPv4, or a fragment thereof.
  • the restorer locus comprises on maize chromosome 3 a genomic interval corresponding to (nucleic acid) position 195629901 to 197698278 of the B73 reference maize genome AGPv4, or a fragment thereof.
  • the restorer locus is flanked on maize chromosome 3 by (nucleic acid) positions corresponding to positions 195629901 and 197698278 of the B73 reference maize genome AGPv4, or a fragment thereof.
  • the restorer locus of the invention is comprised on maize chromosome 3 in a genomic interval corresponding to (nucleic acid) position 197453646 to 198023573 of the B73 reference maize genome AGPv4, or a fragment thereof.
  • the restorer locus comprises on maize chromosome 3 a genomic interval corresponding to (nucleic acid) position 197453646 to 198023573 of the B73 reference maize genome AGPv4, or a fragment thereof.
  • the restorer locus is flanked on maize chromosome 3 by (nucleic acid) positions corresponding to positions 197453646 and 198023573 of the B73 reference maize genome AGPv4, or a fragment thereof.
  • the molecular marker(s) are selected from Table 4 or 5. As indicated in Tables 4 and 5, all markers are polymorphic and are capable of discriminating between the restorer and non-restorer (or maintainer). Accordingly, identification of a restorer entails identification of one or more restorer-associated/linked polymorphisms as indicated in Tables 4 and 5, whereas identification of a non-restorer/maintainer entails identification of one or more non-restorer/maintainer-associated/linked polymorphisms as indicated in Tables 4 and 5.
  • a polynucleic acid or locus of the invention as described herein is said to be flanked by certain molecular markers or molecular marker alleles if the polynucleic acid/locus is comprised within a polynucleic acid wherein respectively a first marker (allele) is located upstream (i.e. 5') of said polynucleic acid and a second marker (allele) is located downstream (i.e. 3') of said polynucleic acid.
  • first and second marker (allele) may border the polynucleic acid.
  • the nucleic acid may equally comprise such first and second marker (allele), such as respectively at or near the 5' and 3' end, for instance respectively within 50 kb of the 5' and 3' end, preferably within 10 kb of the 5' and 3' end, such as within 5 kb of the 5' and 3' end, within 1 kb of the 5' and 3' end, or less.
  • first and second marker allele
  • the methods of the invention for identifying a maize plant or plant part comprise screening for the presence of or detecting or identifying one or more molecular marker (allele) selected from SEQ ID Nos: 17 to 200, wherein n is the corresponding nucleotide for the restorer polymorphism (SNP) (as indicated in Table 4).
  • SNP restorer polymorphism
  • the methods of the invention for identifying a maize plant or plant part comprise screening for the presence of or detecting or identifying one or more molecular marker (allele) selected from SEQ ID Nos: 17 to 200, wherein n is the corresponding nucleotide for the non-restorer/maintainer polymorphism (SNP) (as indicated in Table 4).
  • SNP non-restorer/maintainer polymorphism
  • the methods of the invention for identifying a maize plant or plant part comprise screening for the absence of one or more molecular marker (allele) selected from SEQ ID Nos: 17 to 200, wherein n is the corresponding nucleotide for the restorer polymorphism (SNP) (as indicated in Table 4).
  • allele selected from SEQ ID Nos: 17 to 200, wherein n is the corresponding nucleotide for the restorer polymorphism (SNP) (as indicated in Table 4).
  • the methods of the invention for identifying a maize plant or plant part comprise screening for the absence of one or more molecular marker (allele) selected from SEQ ID Nos: 17 to 200, wherein n is the corresponding nucleotide for the non-restorer/maintainer polymorphism (SNP) (as indicated in Table 4).
  • allele selected from SEQ ID Nos: 17 to 200, wherein n is the corresponding nucleotide for the non-restorer/maintainer polymorphism (SNP) (as indicated in Table 4).
  • the methods of the invention for identifying a maize plant or plant part comprise screening for the presence of or detecting or identifying one or more molecular marker (allele) selected from SEQ ID Nos: 68 to 140, wherein n is the corresponding nucleotide for the restorer polymorphism (SNP) (as indicated in Table 4).
  • SNP restorer polymorphism
  • the methods of the invention for identifying a maize plant or plant part comprise screening for the presence of or detecting or identifying one or more molecular marker (allele) selected from SEQ ID Nos: 68 to 140, wherein n is the corresponding nucleotide for the non-restorer/maintainer polymorphism (SNP) (as indicated in Table 4).
  • SNP non-restorer/maintainer polymorphism
  • the methods of the invention for identifying a maize plant or plant part comprise screening for the absence of one or more molecular marker (allele) selected from SEQ ID Nos: 68 to 140, wherein n is the corresponding nucleotide for the restorer polymorphism (SNP) (as indicated in Table 4).
  • allele selected from SEQ ID Nos: 68 to 140, wherein n is the corresponding nucleotide for the restorer polymorphism (SNP) (as indicated in Table 4).
  • the methods of the invention for identifying a maize plant or plant part comprise screening for the absence of one or more molecular marker (allele) selected from SEQ ID Nos: 68 to 140, wherein n is the corresponding nucleotide for the non-restorer/maintainer polymorphism (SNP) (as indicated in Table 4).
  • allele selected from SEQ ID Nos: 68 to 140, wherein n is the corresponding nucleotide for the non-restorer/maintainer polymorphism (SNP) (as indicated in Table 4).
  • the methods of the invention for identifying a maize plant or plant part comprise screening for the presence of or detecting or identifying one or more molecular marker (allele) selected from SEQ ID Nos: 70, 72, 76, 79, 86, 88, 92, 93, 99, 104, 105, 107, 108, 109, 115, and 134, wherein n is the corresponding nucleotide for the restorer polymorphism (SNP) (as indicated in Table 4).
  • SNP restorer polymorphism
  • the methods of the invention for identifying a maize plant or plant part comprise screening for the presence of or detecting or identifying one or more molecular marker (allele) selected from SEQ ID Nos: 70, 72, 76, 79, 86, 88, 92, 93, 99, 104, 105, 107, 108, 109, 115, and 134, wherein n is the corresponding nucleotide for the non-restorer/maintainer polymorphism (SNP) (as indicated in Table 4).
  • SNP non-restorer/maintainer polymorphism
  • the methods of the invention for identifying a maize plant or plant part comprise screening for the absence of one or more molecular marker (allele) selected from SEQ ID Nos: 70, 72, 76, 79, 86, 88, 92, 93, 99, 104, 105, 107, 108, 109, 115, and 134, wherein n is the corresponding nucleotide for the restorer polymorphism (SNP) (as indicated in Table 4).
  • SNP restorer polymorphism
  • the methods of the invention for identifying a maize plant or plant part comprise screening for the absence of one or more molecular marker (allele) selected from SEQ ID Nos: 70, 72, 76, 79, 86, 88, 92, 93, 99, 104, 105, 107, 108, 109, 115, and 134, wherein n is the corresponding nucleotide for the non-restorer/maintainer polymorphism (SNP) (as indicated in Table 4).
  • SNP non-restorer/maintainer polymorphism
  • the methods of the invention for identifying a maize plant or plant part comprise screening for the presence of or detecting or identifying any one or more of SEQ ID NOs: 1, 5, 9, and 13, or a (unique) fragment thereof, or one or more of SEQ ID NOs: 2, 6, 10, and 14, or a (unique) fragment thereof.
  • the methods of the invention for identifying a maize plant or plant part comprise screening for the presence of or detecting or identifying any one or more of SEQ ID NOs: 1, 5, 9, and 13, or a (unique) fragment thereof, wherein the presence indicates that the plant or plant part is a restorer or comprises a restorer (gene(s), locus (allele), haplotype, genome, or phenotype).
  • the methods of the invention for identifying a maize plant or plant part comprise screening for the presence of or detecting or identifying any one or more of SEQ ID NOs: 1, 5, 9, and 13, or a (unique) fragment thereof, wherein the absence indicates that the plant or plant part is a not a restorer or does not comprise a restorer (gene(s), locus (allele), haplotype, genome, or phenotype).
  • the methods of the invention for identifying a maize plant or plant part comprise screening for the presence of or detecting or identifying any one or more of SEQ ID NOs: 1, 5, 9, and 13, or a (unique) fragment thereof, wherein the absence indicates that the plant or plant part is a maintainer or comprises a maintainer (gene(s), locus (allele), haplotype, genome, or phenotype).
  • the methods of the invention for identifying a maize plant or plant part comprise screening for the presence of or detecting or identifying any one or more of SEQ ID NOs: 2, 6, 10, and 14, or a (unique) fragment thereof, wherein the presence indicates that the plant or plant part is not a restorer or does not comprise a restorer (gene(s), locus (allele), haplotype, genome, or phenotype).
  • the methods of the invention for identifying a maize plant or plant part comprise screening for the presence of or detecting or identifying any one or more of SEQ ID NOs: 2, 6, 10, and 14, or a (unique) fragment thereof, wherein the presence indicates that the plant or plant part is a maintainer or comprises a maintainer (gene(s), locus (allele), haplotype, genome, or phenotype).
  • the methods of the invention for identifying a maize plant or plant part comprise screening for the presence of or detecting or identifying any one or more of SEQ ID NOs: 2, 6, 10, and 14, or a (unique) fragment thereof, wherein the absence indicates that the plant or plant part is a restorer or comprises a restorer (gene(s), locus (allele), haplotype, genome, or phenotype).
  • the invention relates to an (isolated) polynucleic acid comprising any one or more of the sequences, molecular markers or molecular marker alleles as described herein elsewhere, or a fragment thereof, and/or the complement thereof or the reverse complement thereof.
  • the polynucleotide or polynucleic acid according to the invention as described herein is an isolated polynucleotide or polynucleic acid.
  • the invention relates to an (isolated) polynucleic acid comprising a (unique) fragment of any of the sequences, molecular markers or molecular marker alleles as described herein elsewhere, or the complement thereof or the reverse complement thereof.
  • said polynucleic acid is at least 15 nucleotides, more preferably at least 20 nucleotides, such as at least 25, 30, 35, 40, 45, 50, 75, 100, 125, 150, 175, 200 or more nucleotides.
  • the polynucleic acid is at most 500 nucleotides, preferably at most 250 nucleotides, such as at most 200, 150, 100, or 50 nucleotides.
  • the polynucleic acid has from 15 to 500 nucleotides, such as from 20 to 250 nucleotides or from 20 to 100 nucleotides, such as from 20 to 50 nucleotides.
  • the invention relates to an (isolated) polynucleic acid (specifically) hybridizing with any of the sequences, molecular markers or molecular marker alleles as described herein elsewhere, or the complement thereof or the reverse complement thereof.
  • said polynucleic acid is at least 15 nucleotides, more preferably at least 20 nucleotides, such as at least 25, 30, 35, 40, 45, 50, 75, 100, 125, 150, 175, 200 or more nucleotides.
  • the polynucleic acid is at most 500 nucleotides, preferably at most 250 nucleotides, such as at most 200, 150, 100, or 50 nucleotides.
  • the polynucleic acid has from 15 to 500 nucleotides, such as from 20 to 250 nucleotides or from 20 to 100 nucleotides, such as from 20 to 50 nucleotides.
  • the invention relates to a polynucleic acid comprising a molecular marker (allele) of Table 4 or Table 5, or a (unique) fragment thereof, and/or the complement or reverse complement thereof.
  • the invention relates to a polynucleic acid comprising a restorer molecular marker (allele) of Table 4 or Table 5, or a (unique) fragment thereof, and/or the complement or reverse complement thereof.
  • the invention relates to a polynucleic acid comprising a non-restorer/maintainer molecular marker (allele) of Table 4 or Table 5, or a (unique) fragment thereof, and/or the complement or reverse complement thereof.
  • such fragment when reference is made to a fragment of a polynucleic acid or protein, such fragment comprises respectively at least 15 nucleotides or amino acids, preferably at least 20 nucleotides or amino acids.
  • the polynucleic acids according to the invention comprises or specifically hybridizes with one or more of the molecular marker (allele) and additional 5' and/or 3' contiguous nucleotides (naturally) flanking the respective marker (allele) (or the complement or reverse complement thereof).
  • the amount of flanking may in certain embodiments be at least 14 or 15 nucleotides (which may or may not be entirely 5' or entirely 3' flanking nucleotides, such as for instance 5 3' flanking nucleotides plus 10 5' flanking nucleotides.
  • the molecular marker (allele) of the present invention (or the complement thereof) is the most 5' nucleotide of the polynucleic acid.
  • the molecular marker (allele) of the present invention is the second most 5' nucleotide of the polynucleic acid. In certain embodiments, the molecular marker (allele) of the present invention (or the complement thereof) is the third most 5' nucleotide of the polynucleic acid. In certain embodiments, the molecular marker (allele) of the present invention (or the complement thereof) is the most 3' nucleotide of the polynucleic acid. In certain embodiments, the molecular marker (allele) of the present invention (or the complement thereof) is the second most 3' nucleotide of the polynucleic acid.
  • the molecular marker (allele) of the present invention is the third most 3' nucleotide of the polynucleic acid.
  • Such terminally located markers such as SNPs
  • the invention relates to a polynucleic acid comprising or comprised in any of SEQ ID NOs: 1 to 208, or a (unique) fragment thereof, and/or the complement thereof or the reverse complement thereof.
  • the invention relates to a polynucleic acid specifically hybridizing with a polynucleic acid comprising or comprised in any of SEQ ID NOs: 1 to 208, or a (unique) fragment thereof, and/or the complement thereof or the reverse complement thereof.
  • polynucleic acids comprise at least one or more of the polymorphic nucleotides, insertions, deletions, or substitutions of the invention as referred to herein elsewhere and contiguous 5' and/or 3" flanking sequences, as described herein elsewhere.
  • the polynucleic acid comprises or is comprised in any of SEQ ID NOs: 17 to 200, wherein n is the corresponding nucleotide for the restorer polymorphism (SNP) (as indicated in Table 4).
  • SNP restorer polymorphism
  • the polynucleic acid comprises or is comprised in any of SEQ ID Nos: 17 to 200, wherein n is the corresponding nucleotide for the non-restorer/maintainer polymorphism (SNP) (as indicated in Table 4).
  • SNP non-restorer/maintainer polymorphism
  • the polynucleic acid comprises or is comprised in any of SEQ ID Nos: 68 to 140, wherein n is the corresponding nucleotide for the restorer polymorphism (SNP) (as indicated in Table 4).
  • SNP restorer polymorphism
  • the polynucleic acid comprises or is comprised in any of SEQ ID Nos: 68 to 140, wherein n is the corresponding nucleotide for the non-restorer/maintainer polymorphism (SNP) (as indicated in Table 4).
  • SNP non-restorer/maintainer polymorphism
  • the polynucleic acid comprises or is comprised in any of SEQ ID Nos: 70, 72, 76, 79, 86, 88, 92, 93, 99, 104, 105, 107, 108, 109, 115, and 134, wherein n is the corresponding nucleotide for the restorer polymorphism (SNP) (as indicated in Table 4).
  • SNP restorer polymorphism
  • the polynucleic acid comprises or is comprised in any of SEQ ID Nos: 70, 72, 76, 79, 86, 88, 92, 93, 99, 104, 105, 107, 108, 109, 115, and 134, wherein n is the corresponding nucleotide for the non-restorer/maintainer polymorphism (SNP) (as indicated in Table 4).
  • SNP non-restorer/maintainer polymorphism
  • the polynucleic acid comprises or is comprised in any of SEQ ID NOs: 1-3, 5-7, 9-11, 13-15, 201, 203, 205, or 207, or the complement thereof, or the reverse complement thereof, or a (unique) fragment thereof.
  • the polynucleic acid comprises or is comprised in a polynucleic acid encoding a protein of SEQ ID NOs: 4, 8, 12, 16, 202, 204, 206, 208, or the complement thereof, or the reverse complement thereof, or a (unique) fragment thereof.
  • the polynucleic acid comprises or is comprised in any of SEQ ID NOs: 1, 5, 9, 13, 201, 203, 205, or 207, preferably SEQ ID NO: 1 or 201, or the complement thereof, or the reverse complement thereof, or a (unique) fragment thereof.
  • the polynucleic acid comprises or is comprised in a polynucleic acid encoding a protein of SEQ ID NOs: 202, 204, 206, 208, preferably SEQ ID NO: 202, or the complement thereof, or the reverse complement thereof, or a (unique) fragment thereof.
  • the polynucleic acid comprises or is comprised in any of SEQ ID NOs: 2-3, 6-7, 10-11, 14-15, preferably SEQ ID NO: 2, or the complement thereof, or the reverse complement thereof, or a (unique) fragment thereof.
  • the polynucleic acid comprises or is comprised in a polynucleic acid encoding a protein of SEQ ID NOs: 4, 8, 12, 16, preferably SEQ ID NO: 4, or the complement thereof, or the reverse complement thereof, or a (unique) fragment thereof.
  • Such polynucleic acids are suitable for identifying plants or plant parts as well as for generating plants as described herein elsewhere.
  • the polynucleic acid comprises at least 15 nucleotides, such as 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 nucleotides, such as at least 30, 35, 40, 45, or 50 nucleotides, such as at least 100, 200, 300, or 500 nucleotides.
  • the polynucleic acid comprises or consists of a polynucleic acid as defined in numbered statements 27 to 30, referred to herein elsewhere.
  • the polynucleic acid comprises at most 1500 nucleotides, such as 1200, 1000, 800, 600, 400, 200 nucleotides, such as at most 100, 80, 60, 50, 40, or 30 nucleotides.
  • the polynucleic acid comprises at least 15 nucleotides, such as 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 nucleotides, such as at least 30, 35, 40, 45, or 50 nucleotides, such as at least 100, 200, 300, or 500 nucleotides, and the polynucleic acid comprises at most 1500 nucleotides, such as 1200, 1000, 800, 600, 400, 200 nucleotides, such as at most 100, 80, 60, 50, 40, or 30 nucleotides.
  • the (isolated) polynucleotide has a length ranging from 15 to 500 nucleotides, preferably 15 to 100 nucleotides, preferably 15 to 50 nucleotides, more preferably 15 to 35 nucleotides.
  • the (isolated) polynucleotide is a primer or a probe.
  • the (isolated) polynucleotide is an allele-specific primer or probe.
  • the (isolated) is a KASP (Kompetitive allele specific PCR) primer.
  • Primers including KASP primers, are well-known in the art and can be designed by the skilled person according to known criteria.
  • KASP is performed with two (or more) allele-specific primers (which may be the forward primers) and generally one common primer (which may be the reverse primer).
  • the allele-specific primers are typically elongated with tail sequences (in which a different tail sequence is provided for each allele-specific primer). The tail sequences allow incorporation of a fluorescently labelled complementary sequence, to thereby fluorescently distinguish the different alleles.
  • the length of the tail sequence is comprised in the total primer length. In certain embodiments, the length of the tail sequence is not comprised in the total primer length.
  • the polynucleic acid is a (PCR) primer or (hybridization) probe. In certain embodiments, the polynucleic acid is an allele-specific primer or probe. In certain embodiments, the polynucleic acid is a KASP primer.
  • the invention relates to a (isolated) polynucleic acid comprising a (molecular) marker (allele) of the invention, or the complement or the reverse complement of a (molecular) marker (allele) of the invention.
  • the invention relates to a polynucleic acid comprising at least 10 contiguous nucleotides, preferably at least 15 contiguous nucleotides or at least 20 contiguous nucleotides of a (molecular) marker (allele) of the invention, or the complement or the reverse complement of a (molecular) marker (allele) of the invention.
  • the polynucleic acid is capable of discriminating between a (molecular) marker (allele) of the invention and a non-molecular marker allele, such as to specifically hybridise with a (molecular) marker allele of the invention.
  • the polynucleic acid or the complement or reverse complement thereof does not (substantially) hybridise with or bind to (genomic) DNA originating from maize inbred line B73.
  • the sequence of the polynucleic acid or the complement or reverse complement thereof does not occur or is not present in maize inbred line B73.
  • the invention relates to a kit comprising one or more of the polynucleotides as described herein, such as one or more of the primers or probes as described herein.
  • the polynucleotides may be comprised for instance in a single receptacle, such as a single vial, or in separate receptacles, such as separate vials.
  • hybridizing means that the polynucleic acid hybridises with the (molecular) marker allele (such as under stringent hybridisation conditions, as defined herein elsewhere), but does not (substantially) hybridise with a polynucleic acid not comprising the marker allele or is (substantially) incapable of being used as a PCR primer.
  • the hybridization signal with the marker allele or PCR amplification of the marker allele is at least 5 times, preferably at least 10 times stronger or more than the hybridisation signal with a non-marker allele, or any other sequence.
  • the invention relates to a set of primers or probes as described above, such as a set of allele-specific primers or probes.
  • the set may further comprise a (common) forward or reverse primer (depending on whether the allele-specific primers are reverse or forward primers).
  • the invention relates to a kit comprising such polynucleic acids, such as primers (comprising forward (such as one or more allele-specific or alternatively common primers) and/or reverse primers (such as a common or alternatively one or more allele-specific primers)) and/or probes (such as one or more allele-specific probe).
  • primers comprising forward (such as one or more allele-specific or alternatively common primers) and/or reverse primers (such as a common or alternatively one or more allele-specific primers)) and/or probes (such as one or more allele-specific probe).
  • primers comprising forward (such as one or more allele-specific or alternatively common primers) and/or reverse primers (such as a common or alternatively one or more allele-specific primers)) and/or probes (such as one or more allele-specific probe).
  • probes such as one or more allele-specific probe.
  • both primers forward or reverse
  • the other primer may or may not be capable of discriminating between a (molecular) marker allele of the invention and a non-marker allele, and hence may or may not be unique.
  • the invention relates to a vector comprising a (isolated) polynucleic acid according to the invention as described herein.
  • the vector is a (plant) expression vector.
  • the vector is an inducible (plant) expression vector.
  • the expression is tissue- or organ-specific.
  • the expression is developmentally specific.
  • the expression is tissue- or organ-specific and developmentally specific.
  • the vector comprises any of SEQ ID NOs: 1-3, 5-7, 9-11, 13-15, 201, 203, 205, or 207, or the complement thereof, or the reverse complement thereof, or a (unique) fragment thereof.
  • the vector comprises a polynucleic acid encoding a protein of SEQ ID NOs: 4, 8,12,16, 202, 204, 206, 208, or the complement thereof, or the reverse complement thereof, or a (unique) fragment thereof.
  • the vector comprises any of SEQ ID NOs: 1, 5, 9, 13, 201, 203, 205, or 207, preferably SEQ ID NO: 1 or 201, or the complement thereof, or the reverse complement thereof, or a (unique) fragment thereof.
  • the vector comprises a polynucleic acid encoding a protein of SEQ ID NOs: 202, 204, 206, 208, preferably SEQ ID NO: 202, or the complement thereof, or the reverse complement thereof, or a (unique) fragment thereof.
  • the vector comprises any of SEQ ID NOs: 2-3, 6-7, 10-11, 14-15, preferably SEQ ID NO: 2, or the complement thereof, or the reverse complement thereof, or a (unique) fragment thereof.
  • the vector comprises a polynucleic acid encoding a protein of SEQ ID NOs: 4, 8, 12, 16, preferably SEQ ID NO: 4, or the complement thereof, or the reverse complement thereof, or a (unique) fragment thereof.
  • polynucleic acids are suitable for identifying plants or plant parts as well as for generating plants as described herein elsewhere.
  • a "vector” has its ordinary meaning in the art, and may for instance be a plasmid, a cosmid, a phage or an expression vector, a transformation vector, shuttle vector, or cloning vector; it may be double- or single-stranded, linear or circular; or it may transform a prokaryotic or eukaryotic host, either via integration into its genome or extrachromosomally.
  • the nucleic acid according to the invention is preferably operatively linked in a vector with one or more regulatory sequences which allow the transcription, and, optionally, the expression, in a prokaryotic or eukaryotic host cell.
  • a regulatory sequence - preferably DNA - may be homologous or heterologous to the nucleic acid according to the invention.
  • the nucleic acid is under the control of a suitable promoter or terminator.
  • Suitable promoters may be promoters which are constitutively induced (example: 35S promoter from the "Cauliflower mosaic virus" (Odell et al., 1985); those promoters which are tissue-specific are especially suitable (example: Pollen-specific promoters, Chen et al. (2010), Zhao et al. (2006), or Twell et al. (1991)), or are development-specific (example: blossom-specific promoters).
  • Suitable promoters may also be synthetic or chimeric promoters which do not occur in nature, are composed of multiple elements, and contain a minimal promoter, as well as - upstream of the minimum promoter - at least one cis-regulatory element which serves as a binding location for special transcription factors.
  • Chimeric promoters may be designed according to the desired specifics and are induced or repressed via different factors. Examples of such promoters are found in Gurr & Rushton (2005) or Venter (2007).
  • a suitable terminator is the nos-terminator (Depicker et al., 1982).
  • the vector may be introduced via conjugation, mobilization, biolistic transformation, agrobacteria-mediated transformation, transfection, transduction, vacuum infiltration, or electroporation.
  • the vector may be a plasmid, a cosmid, a phage or an expression vector, a transformation vector, shuttle vector, or cloning vector; it may be double- or single-stranded, linear or circular.
  • the vector may transform a prokaryotic or eukaryotic host, either via integration into its genome or extrachromosomally.
  • operatively linked or "operably linked” means connected in a common nucleic acid molecule in such a manner that the connected elements are positioned and oriented relative to one another such that a transcription of the nucleic acid molecule may occur.
  • a DNA which is operatively linked with a promoter is under the transcriptional control of this promoter.
  • the invention relates to the use of the polynucleic acid or vector according to the invention as described herein for generating a maize plant or plant part, such as a maize plant or plant part having increased pathogen resistance and/or tolerance.
  • the vector is an expression vector.
  • the nucleic acid is preferably operatively linked in a vector with one or more regulatory sequences which allow the transcription, and optionally the expression, in a prokaryotic or eukaryotic host cell.
  • a regulatory sequence may be homologous or heterologous to the nucleic acid.
  • the nucleic acid is under the control of a suitable promoter or terminator.
  • Suitable promoters may be promoters which are constitutively induced, for example, the 35S promoter from the "Cauliflower mosaic virus" (Odell et al., 1985. Identification of DNA sequences required for activity of the cauliflower mosaic virus 35S promoter.) Tissue-specific promoters, e.g.
  • pollen-specific promoters as described in Chen et al. (2010. Molecular Biology Reports 37(2):737-744 ), Zhao et al. (2006. Planta 224(2): 405-412 ), or Twell et al. (1991. Genes & Development 5(3): 496-507 ), are particularly suitable, as are development-specific promoters, e.g. blossom-specific promoters.
  • Suitable promoters may also be synthetic or chimeric promoters which do not occur in nature, and which are composed of multiple elements. Such synthetic or chimeric promoter may contain a minimal promoter, as well as at least one cis-regulatory element which serves as a binding location for special transcription factors.
  • Chimeric promoters may be designed according to the desired specifics and can be induced or repressed via different factors. Examples of such promoters are found in Gurr & Rushton (2005. Trends in Biotechnology 23(6): 275-282 ) or Venter (2007. Trends in Plant Science: 12(3):, 118-124 ). For example, a suitable terminator is the nos-terminator ( Depicker et al., 1982. Journal of Molecular and Applied Genetics 1(6): 561-573 ).
  • the vector is a conditional expression vector. In certain embodiments, the vector is a constitutive expression vector. In certain embodiments, the vector is a tissue-specific expression vector, such as a pollen-specific expression vector. In certain embodiments, the vector is an inducible expression vector. All such vectors are well-known in the art. Methods for preparation of the described vectors are commonplace to the person skilled in the art (Sambrook et al., 2001).
  • a host cell such as a plant cell, which comprises a nucleic acid as described herein, preferably an induction-promoting nucleic acid or a nucleic acid encoding a double-stranded RNA as described herein, or a vector as described herein.
  • the host cell may contain the nucleic acid as an extra-chromosomally (episomal) replicating molecule, or comprises the nucleic acid integrated in the nuclear or plastid genome of the host cell, or as introduced chromosome, e.g. minichromosome.
  • the host cell may be a prokaryotic (for example, bacterial) or eukaryotic cell (for example, a plant cell or a yeast cell).
  • the host cell may be an agrobacterium, such as Agrobacterium tumefaciens or Agrobacterium rhizogenes.
  • the host cell is a plant cell.
  • the invention relates to the use of the polynucleic acid or vector according to the invention as described herein for identifying a maize plant or plant part, such as a maize plant or plant part having increased pathogen resistance and/or tolerance.
  • a nucleic acid described herein or a vector described herein may be introduced in a host cell via well-known methods, which may depend on the selected host cell, including, for example, conjugation, mobilization, biolistic transformation, agrobacteria-mediated transformation, transfection, transduction, vacuum infiltration, or electroporation.
  • methods for introducing a nucleic acid or a vector in an agrobacterium cell are well-known to the skilled person and may include conjugation or electroporation methods.
  • methods for introducing a nucleic acid or a vector into a plant cell are known (Sambrook et al., 2001) and may include diverse transformation methods such as biolistic transformation and agrobacterium-mediated transformation.
  • the present invention relates to a transgenic plant cell which comprises a nucleic acid as described herein, in particular an induction-promoting nucleic acid or a nucleic acid encoding a double-stranded RNA as described herein, as a transgene or a vector as described herein.
  • the present invention relates to a transgenic plant or a part thereof which comprises the transgenic plant cell.
  • such a transgenic plant cell or transgenic plant is a plant cell or plant which is, preferably stably, transformed with a nucleic acid as described herein, in particular an induction-promoting nucleic acid or a nucleic acid encoding a double-stranded RNA as described herein, or a vector as described herein.
  • the nucleic acid in the transgenic plant cell is operatively linked with one or more regulatory sequences which allow the transcription, and optionally the expression, in the plant cell.
  • a regulatory sequence may be homologous or heterologous to the nucleic acid.
  • the total structure made up of the nucleic acid according to the invention and the regulatory sequence(s) may then represent the transgene.
  • the invention relates to the use of one or more of the (molecular) marker (allele) described herein for identifying a plant or plant part having a fertility restorer (gene, locus, haplotype, genotype, or phenotype).
  • the invention relates to the use of one or more of the (molecular) marker (allele) described herein which are able to detect at least one diagnostic marker allele for identifying a plant or plant part, such as having having a fertility restorer (gene, locus, haplotype, genotype, or phenotype).
  • the invention relates to the detection of one or more of the (molecular) marker alleles described herein for identifying a plant or plant part having having a fertility restorer (gene, locus, haplotype, genotype, or phenotype).
  • the invention relates to a (maize) plant or plant part identified by the methods of the invention as described herein.
  • this includes plant material obtained from said plant or plant part.
  • the invention relates to a (maize) plant or plant part comprising one or more of the (molecular) markers (alleles), polynucleic acids, loci, or vectors of the invention as described herein.
  • the invention relates to a (maize) plant or plant part comprising one or more of the (molecular) marker (alleles) of Table 4 or 5.
  • the invention relates to a (maize) plant or plant part comprising one or more polynucleic acid of SEQ ID NO: 1 to 208. In an aspect, the invention relates to a (maize) plant or plant part comprising one or more polynucleic acid of SEQ ID NO: 17 to 200. In certain embodiments, the polynucleic acid of SEQ ID Nos: 17-200 corresponds to a polynucleic acid of a restorer of the invention. In certain embodiments, the polynucleic acid of SEQ ID Nos: 17-200 corresponds to a polynucleic acid of a non-restorer/maintainer of the invention.
  • the invention relates to a (maize) plant or plant part comprising one or more polynucleic acid of SEQ ID NO: 68 to 140.
  • the invention relates to a (maize) plant or plant part comprising one or more polynucleic acid of SEQ ID NO: 70, 72, 76, 79, 86, 88, 92, 93, 99, 104, 105, 107, 108, 109, 115, and/or 134.
  • the invention relates to a (maize) plant or plant part comprising one or more polynucleic acid of SEQ ID NO: 1, 5, 9, or 13 or one or more of SEQ ID NOs: 2, 6, 10, and 14.
  • the invention relates to a (maize) plant or plant part comprising one or more polynucleic acid encoding Zm00001d043358, Zm00001d043352, Zm00001d043356, and Zm00001d043357, having respectively a coding sequence as set forth in any of SEQ ID NOs: 201, 203, 205, and 207, or having respectively a coding sequence as set forth in any of SEQ ID NOs: 3, 7, 11, and 15.
  • the invention relates to a (maize) plant or plant part comprising one or more polypeptide having a sequence as set forth in any of SEQ ID NOs: 202, 204, 206, or 208, or having a sequence as set forth in any of SEQ ID NOs: 4, 8, 12, or 16.
  • the plant or plant part comprises a polynucleic acid encoding the polypeptide, which may be provided on a vector or may be genomically integrated.
  • the markers (alleles), polynucleic acids, or loci as defined herein are homozygous. Accordingly, in diploid plants the two alleles are identical (at least with respect to the particular marker (allele), polynucleic acid, or locus), in tetraploid plants the four alleles are identical, and in hexaploid plants the six alleles are identical with respect to the marker (allele), polynucleic acid, or locus. In certain embodiments, the marker (allele), polynucleic acid, or locus as defined herein is heterozygous.
  • the two alleles are not identical, in tetraploid plants the four alleles are not identical (for instance only one, two, or three alleles comprise the specific marker (allele), polynucleic acid, or locus), and in hexaploid plants the six alleles are not identical with respect to the mutation or marker (for instance only one, two, three, four or five alleles comprise the specific marker (allele), polynucleic acid, or locus). Similar considerations apply in case of pseudopolyploid pants.
  • the invention relates to a method for generating a (maize) plant or plant part comprising introducing in (the genome of) said plant or plant part a polypeptide, polynucleic acid, locus (allele), or (molecular) marker (allele) of the invention as defined herein, or a (functional) fragment thereof.
  • introduction into the plant or plant part is genomic introduction.
  • introduction is non-genomic introduction, such as episomal introduction.
  • introduction is achieved by means of a vector, as is known in the art and as also described herein elsewhere.
  • the invention relates to a method for generating a (maize) plant or plant part comprising introducing in (the genome of) said plant or plant part one or more polynucleic acid of SEQ ID NO: 1 to 208.
  • the invention relates to a method for generating a (maize) plant or plant part comprising introducing in (the genome of) said plant or plant part one or more polynucleic acid of SEQ ID NO: 17 to 200.
  • the polynucleic acid of SEQ ID Nos: 17-200 corresponds to a polynucleic acid of a restorer of the invention.
  • the polynucleic acid of SEQ ID Nos: 17-200 corresponds to a polynucleic acid of a non-restorer/maintainer of the invention.
  • the skilled person will appreciate that the discrimination between restorer and non-restorer/maintainer can be made based on the identity of "n" in SEQ ID Nos 17-200, as also described herein elsewhere (such as for instance based on Table 4).
  • the invention relates to a method for generating a (maize) plant or plant part comprising introducing in (the genome of) said plant or plant part one or more polynucleic acid of SEQ ID NO: 68 to 140.
  • the invention relates to a method for generating a (maize) plant or plant part comprising introducing in (the genome of) said plant or plant part one or more polynucleic acid of SEQ ID NO: 70, 72, 76, 79, 86, 88, 92, 93, 99, 104, 105, 107, 108, 109, 115, and/or 134.
  • the invention relates to a method for generating a (maize) plant or plant part comprising introducing in (the genome of) said plant or plant part one or more polynucleic acid of SEQ ID NO: 1, 5, 9, or 13 or one or more of SEQ ID NOs: 2, 6, 10, and 14.
  • the invention relates to a method for generating a (maize) plant or plant part comprising introducing in (the genome of) said plant or plant part one or more polynucleic acid encoding Zm00001d043358, Zm00001d043352, Zm00001d043356, and Zm00001d043357, having respectively a coding sequence as set forth in any of SEQ ID NOs: 201, 203, 205, and 207, or having respectively a coding sequence as set forth in any of SEQ ID NOs: 3, 7, 11, and 15.
  • the invention relates to a method for generating a (maize) plant or plant part comprising introducing in said plant or plant part one or more polypeptide having a sequence as set forth in any of SEQ ID NOs: 202, 204, 206, or 208, or having a sequence as set forth in any of SEQ ID NOs: 4, 8, 12, or 16.
  • the plant or plant part comprises a polynucleic acid encoding the polypeptide, which may be provided on a vector or may be genomically integrated.
  • the invention relates to a method for generating a (maize) plant or plant part comprising introducing in (the genome of) said plant or plant part one or more polynucleic acid encoding a polypeptide having a sequence as set forth in any of SEQ ID NOs: 202, 204, 206, or 208, or having a sequence as set forth in any of SEQ ID NOs: 4, 8, 12, or 16.
  • introducing (into the genome) as referred to herein comprises transgenesis.
  • introducing (into the genome) as referred to herein comprises transformation.
  • introducing (into the genome) as referred to herein comprises recombination, such as homologous recombination.
  • introducing (into the genome) as referred to herein comprises mutagenesis.
  • introducing (into the genome) as referred to herein comprises introgression. In certain embodiments, introducing into the genome as referred to herein does not comprise introgression.
  • introducing into the genome as referred to herein comprises introducing into the genome in a plant part.
  • the plant part is a plant organ.
  • the plant part is a plant tissue.
  • the plant part is a plant cell.
  • the plant part is a protoplast.
  • introducing into the genome as referred to herein comprises introducing into the genome in vitro. In certain embodiments, introducing into the genome as referred to herein comprises introducing into the genome in vivo.
  • the method for generating a maize plant or plant part comprises transforming a plant or plant part, preferably a plant cell, more preferably a protoplast, with a polynucleic acid as described herein elsewhere, and optionally regenerating a plant from said plant cell, preferably protoplast.
  • the transformed plant or plant part does not endogenously comprise the polynucleic acid according to the invention as described herein.
  • the transformed plant or plant part does not endogenously comprise the one or more molecular marker (alleles) according to the invention as described herein.
  • the methods for obtaining or generating plants or plant parts as described herein according to the invention involve or comprise transgenesis and/or gene editing, such as including CRISPR/Cas, TALEN, ZFN, meganucleases; (induced) mutagenesis, which may or may not be random mutagenesis, such as TILLING.
  • transgenesis and/or gene editing such as including CRISPR/Cas, TALEN, ZFN, meganucleases
  • (induced) mutagenesis which may or may not be random mutagenesis, such as TILLING.
  • the methods for obtaining plants or plant parts as described herein according to the invention do not involve or comprise transgenesis, gene editing, and/or mutagenesis.
  • the methods for obtaining plants or plant parts as described herein according to the invention involve, comprise or consist of breeding and/or selection.
  • the methods for obtaining plants or plant parts as described herein according to the invention do not involve, comprise or consist of breeding.
  • the invention relates to a maize plant or plant part obtained or obtainable by the methods according to the invention as described herein, such as the methods for identifying a maize plant or plant part or the methods for generating a maize plant or plant part.
  • the invention also relates to the progeny of such plants.
  • the invention relates to a maize plant or plant part comprising a polynucleic acid according to the invention as described herein.
  • the polynucleic acid allele is homozygous. In certain embodiments, the polynucleic acid allele is heterozygous.
  • the invention relates to a maize plant or plant part comprising any one or more molecular marker (allele) according to the invention as described herein.
  • the molecular marker (allele) is homozygous. In certain embodiments, the molecular marker (allele) allele is heterozygous.
  • the maize plant is not a maize variety. In certain embodiments, the plant is not exclusively obtained by means of an essentially biological process. In certain embodiments, the plant is obtained by a method which contains at least one step other than crossing, i.e. the screening for the presence of a polynucleotide as described herein.
  • such (maize) plant or plant part does not comprise endogenously the recited polynucleic acids.
  • the maize plant or plant part is transgenic, gene-edited, or mutagenized. In certain embodiments, the maize plant or plant part is transgenic, gene-edited, or mutagenized in order to comprise the one or more molecular marker (allele), or one or more of the polynucleic acids according to the invention as described herein.
  • the invention relates to a method for generating a (maize) plant or plant part, comprising (a) providing a first (maize) plant according to the invention or identified according to the invention or generated according to the invention, (b) crossing said first (maize) plant with a second maize plant having cytoplasmic male sterility; and optionally (d) harvesting said (maize) plant part from the progeny.
  • the invention relates to a method for generating a (maize) plant or plant part, comprising (a) providing a first (maize) plant according to the invention or identified according to the invention or generated according to the invention, (b) crossing said first (maize) plant with a second maize plant having cytoplasmic male sterility; and optionally (d) harvesting said (maize) plant part from the progeny, wherein said first plant is a restorer (preferably a restorer of the present invention).
  • the invention relates to a method for generating a (maize) plant or plant part, comprising (a) providing a first (maize) plant according to the invention or identified according to the invention or generated according to the invention, (b) crossing said first (maize) plant with a second maize plant having cytoplasmic male sterility; and optionally (d) harvesting said (maize) plant part from the progeny, wherein said second plant is a restorer (preferably a restorer of the present invention).
  • the invention relates to a method for generating a (maize) plant or plant part, comprising (a) providing a first (maize) plant according to the invention or identified according to the invention or generated according to the invention, (b) crossing said first (maize) plant with a second maize plant having cytoplasmic male sterility; and optionally (d) harvesting said (maize) plant part from the progeny, wherein said first plant is a not a restorer (preferably not a restorer of the present invention).
  • the invention relates to a method for generating a (maize) plant or plant part, comprising (a) providing a first (maize) plant according to the invention or identified according to the invention or generated according to the invention, (b) crossing said first (maize) plant with a second maize plant having cytoplasmic male sterility; and optionally (d) harvesting said (maize) plant part from the progeny, wherein said second plant is a not a restorer (preferably not a restorer of the present invention).
  • the invention relates to a method for generating a (maize) plant or plant part, comprising (a) providing a first (maize) plant according to the invention or identified according to the invention or generated according to the invention, (b) crossing said first (maize) plant with a second maize plant having cytoplasmic male sterility; and optionally (d) harvesting said (maize) plant part from the progeny, wherein said first plant is a restorer (preferably a restorer of the present invention) and wherein said second plant is not a restorer (preferably not a restorer of the present invention).
  • a restorer preferably a restorer of the present invention
  • said second plant is not a restorer (preferably not a restorer of the present invention).
  • the invention relates to a method for generating a (maize) plant or plant part, comprising (a) providing a first (maize) plant according to the invention or identified according to the invention or generated according to the invention, (b) crossing said first (maize) plant with a second maize plant having cytoplasmic male sterility; and optionally (d) harvesting said (maize) plant part from the progeny, wherein said first plant is a not a restorer (preferably not a restorer of the present invention) and wherein said second plant is a restorer (preferably a restorer of the present invention).
  • haplotype A The restoring fraction of haplotype A can only be explained by further minor restorers which could not be identified until now.
  • the region on chromosome 3 contains 6 genes according the AGPv4 annotation https://www.maizegdb.org/genome/assembly/Zm-B73-REFERENCE-GRAMENE-4.0), 4 of them being expressed in pollen, one being involved in mitochondrial organization and thus representing the most prominent candidate gene (Zm00001d043358). All four genes are polymorphic between the two haplotypes.
  • Table 3 List of candidate genes Gene Function SEQ ID NO: Restorer haplotype Reference B73 genomic DNA cDNA protein genomic DNA cDNA protein Zm00001 d 043358 mitochond rion emergei on 1 201 202 2 3 4 Zm00001 d 043352 rRNA processin g 5 203 204 6 7 8 Zm00001 d 043356 aromatic amino acid family biosyntheti c process 9 205 206 10 11 12 Zm00001 d 043357 Plastocya nin-like, Electron carrier 13 207 208 14 15 16
  • 16 KASP markers (Table 4: identifier 54, 56, 60, 63, 70, 72, 76, 77, 83, 88, 89, 91, 92, 93, 99, and 118) were developed which can be used to detect the haplotype, partly by conversion of 600k markers, partly by using new SNPs within the candidate genes.
  • Figs. 2-5 show sequence alignments of the genomic DNA of the candidate genes derived from the RF-03-01 restorer genotype and from a reference genotype (B73). Highlighted in black with white letters are polymorphisms which are additionally suitable to detect undesired restorer genotype.
  • markers with the identifiers 52-124 showed to be 100% associated to the restorer locus on chromosome 3.
  • the region from position 197453646 to 197698278 referenced to B73 AGPv4 is most suitable as target site for marker-associated identification of RF-03-01 restorer genotype.
  • Markers with identifiers 1-51 and 125-184 corresponding to regions from position 195629901 to 196989408 and from position 197708137 to 198023573 can also be used for identification, because the underlying polymorphisms can be found in most genotypes (major alleles), however it is not 100% linked.
  • RF-03-01 is also present in the flint pool used as male, although its impact to restoration is lower than in pool 4. Anyhow, also in this pool a good knowledge of restorer genes should be achieved, because restoring male lines are important for the usefulness of cms. In case only RF-03-01 is present, but not RF4, the restoration may be too weak or may fail in some environments, because this restorer is not as stable as RF4. Therefore, a good genotyping approach in addition to phenotyping is important to secure production. Table 4: List of markers; marker sequences can be found in sequence listing under respective SEQ ID NO as indicated in last column.

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CA3202093A CA3202093A1 (fr) 2020-12-22 2021-12-22 Procedes d'identification et de selection de plante de mais presentant une resistance au gene restaurateur de sterilite male
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WO2012047595A2 (fr) 2010-10-06 2012-04-12 Dow Agrosciences Llc Gène rf4 restaurateur de type c de la stérilité mâle cytoplasmique du maïs (cms), marqueurs moléculaires et leur utilisation

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* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2012047595A2 (fr) 2010-10-06 2012-04-12 Dow Agrosciences Llc Gène rf4 restaurateur de type c de la stérilité mâle cytoplasmique du maïs (cms), marqueurs moléculaires et leur utilisation

Non-Patent Citations (21)

* Cited by examiner, † Cited by third party
Title
"Antibodies, a Laboratory Manual; and Animal Cell Culture", 1988
"DNA technology include Molecular Cloning: A Laboratory Manual", vol. 1-3, 1989, COLD SPRING HARBOR
"General principles of microbiology are set forth", 1987
"PCR 2: A Practical Approach", 1995
AUSUBEL ET AL.: "Current Protocols in Molecular Biology", 1992, GREENE PUBLISHING AND WILEY-INTERSCIENCE
CHEN ET AL., MOLECULAR BIOLOGY REPORTS, vol. 37, no. 2, 2010, pages 737 - 744
DATABASE EMBL [online] 1 October 2007 (2007-10-01), "Zea mays chromosome 3 clone CH201-260F14, *** SEQUENCING IN PROGRESS ***, 20 unordered pieces.", XP002803189, retrieved from EBI accession no. EM_HTG:AC211583 Database accession no. AC211583 *
DAVIS, B. D. ET AL.: "Microbiology", 1980, HARPER & ROW
DEPICKER ET AL., JOURNAL OF MOLECULAR AND APPLIED GENETICS, vol. 1, no. 6, 1982, pages 561 - 573
GURRRUSHTON, TRENDS IN BIOTECHNOLOGY, vol. 23, no. 6, 2005, pages 275 - 282
INNIS ET AL.: "PCR Protocols: A Guide to Methods and Applications", 1990, ACADEMIC PRESS
JIAO YINPING ET AL: "Improved maize reference genome with single-molecule technologies", NATURE, MACMILLAN JOURNALS LTD., ETC, LONDON, vol. 546, no. 7659, 1 June 2017 (2017-06-01), pages 524 - 527, XP037023014, ISSN: 0028-0836, [retrieved on 20170612], DOI: 10.1038/NATURE22971 *
MCCALLUM ET AL.: "Targeted screening for induced mutations", NAT BIOTECHNOL, vol. 18, no. 4, pages 455 - 7, XP055570446, DOI: 10.1038/74542
MCCALLUM ET AL.: "Targeting induced local lesions IN genomes (TILLING) for plant functional genomics", PLANT PHYSIOL., vol. 123, no. 2, June 2000 (2000-06-01), pages 439 - 42
S. GABAY-LAUGHNAN ET AL: "Molecular-Genetic Characterization of CMS-S Restorer-of-Fertility Alleles Identified in Mexican Maize and Teosinte", GENETICS, vol. 166, no. 2, 1 February 2004 (2004-02-01), US, pages 959 - 970, XP055355585, ISSN: 0016-6731, DOI: 10.1534/genetics.166.2.959 *
SAMBROOK ET AL.: "Molecular Cloning. A Laboratory Manual", 2001, COLD SPRING HARBOR LABORATORY PRESS
SCHNABLE, P. S.WISE, R. P.: "The molecular basis of cytoplasmic male sterility and fertility restoration", TRENDS IN PLANT SCIENCE, vol. 3, no. 5, 1998, pages 175 - 180, XP055063075, DOI: 10.1016/S1360-1385(98)01235-7
TWELL ET AL., GENES & DEVELOPMENT, vol. 5, no. 3, 1991, pages 496 - 507
VENTER, TRENDS IN PLANT SCIENCE, vol. 12, no. 3, 2007, pages 118 - 124
YONGMING LIU ET AL: "A preliminary identification of Rf*-A619 , a novel restorer gene for CMS-C in maize ( Zea mays L.)", PEERJ, vol. 4, 1 January 2016 (2016-01-01), pages e2719 - e2719, XP055808494, ISSN: 2167-8359, Retrieved from the Internet <URL:https://peerj.com/articles/2719.html> [retrieved on 20210527], DOI: 10.7717/peerj.2719 *
ZHAO ET AL., PLANTA, vol. 224, no. 2, 2006, pages 405 - 412

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